Add a tutorial about initial and terminal state inference.

[Marius1311]

This adds a new tutorial for initial and terminal state identification.

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[Marius1311]

Hi @michalk8, I still have to add this new pancreas dataset version to figshare and change this to use myst, but otherwise this is finally ready for your review.

[Marius1311]

Test are failing due to scVelo, I partially addressed this in https://github.com/theislab/scvelo/pull/1059, but https://github.com/theislab/scvelo/issues/1044 is still not covered.

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michalk8 commented on 2023-06-13T01:10:26Z ----------------------------------------------------------------

I wouldn't give this a priority over the paragraph below.

Marius1311 commented on 2023-06-13T14:18:57Z ----------------------------------------------------------------

makes sense. I moved it.

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michalk8 commented on 2023-06-13T01:10:27Z ----------------------------------------------------------------

Headings are too high, should be lower than Computing initial and terminal states

This holds also in the CytoTRACE tutorial and the Pseudotime tutorial.

Marius1311 commented on 2023-06-13T14:19:11Z ----------------------------------------------------------------

yes, I'll change this everywhere.

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michalk8 commented on 2023-06-13T01:10:28Z ----------------------------------------------------------------

The sentence "This tutorial does not depend" is too long, would split at "you may"

Would also rephrase (from negative to positive) and mention that this tutorial works with every other kernel + highlight this in bold.

Marius1311 commented on 2023-06-13T14:24:54Z ----------------------------------------------------------------

ok.

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michalk8 commented on 2023-06-13T01:10:29Z ----------------------------------------------------------------

you will need... -> you will need:

Please link to the other tutorials when mentioning the other kernels

Marius1311 commented on 2023-06-13T14:29:15Z ----------------------------------------------------------------

done.

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michalk8 commented on 2023-06-13T01:10:30Z ----------------------------------------------------------------

Would move to the note where you discuss the scverse forum.

Marius1311 commented on 2023-06-13T14:29:38Z ----------------------------------------------------------------

I moved it to the first paragraph.

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michalk8 commented on 2023-06-13T01:10:31Z ----------------------------------------------------------------

Line #4.    from scipy.stats import ttest_ind

Would slighly prefer import scipy.stats as st

_Marius1311 commented on 2023-06-13T15:15:34Z_ ----------------------------------------------------------------

ok, adapted.

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michalk8 commented on 2023-06-13T01:10:31Z ----------------------------------------------------------------

Use ~ when referring to anndata.AnnData.

"When you use a kernel to compute a transition matrix, this matrix, as well as a few informations about the computation, are written "

^ is not completely true, you have to call write_to_adata, maybe mention this.

Marius1311 commented on 2023-06-13T15:17:21Z ----------------------------------------------------------------

done, thanks!

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michalk8 commented on 2023-06-13T01:10:32Z ----------------------------------------------------------------

The {mod}~cellrank.estimators allowo you to analyze cell-state dynamics. We initialize the GPCCA estimator...

However, this and other estimators with with every CellRank {mod}kernel <cellrank.kernels>.

Marius1311 commented on 2023-06-13T15:19:53Z ----------------------------------------------------------------

ok.

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michalk8 commented on 2023-06-13T01:10:33Z ----------------------------------------------------------------

as we explain -> as explained

Marius1311 commented on 2023-06-13T15:20:53Z ----------------------------------------------------------------

well...

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michalk8 commented on 2023-06-13T01:10:34Z ----------------------------------------------------------------

"We'll demonstrate both modes in this tutorial."

There's a way to add links to section headers in myst, see, e.g., here: https://myst-parser.readthedocs.io/en/latest/syntax/cross-referencing.html#implicit-targets

{meth}schur decomposition-> {meth}Schur decomposition

Marius1311 commented on 2023-06-13T15:26:19Z ----------------------------------------------------------------

ok, done.

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michalk8 commented on 2023-06-13T01:10:35Z ----------------------------------------------------------------

Add links to fit() and predict() using the {meth} role.

Marius1311 commented on 2023-06-13T15:26:52Z ----------------------------------------------------------------

I removed these from the section heading.

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michalk8 commented on 2023-06-13T01:10:36Z ----------------------------------------------------------------

Two spaces in "algorithm as"

as implemented in the pyGPCCA package (cite the zenodo)

Marius1311 commented on 2023-06-13T15:27:43Z ----------------------------------------------------------------

included already (reuter:22)

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michalk8 commented on 2023-06-13T01:10:38Z ----------------------------------------------------------------

CellRank corases-grains -> CellRank coarse-grains.

If I remember correctly, cellrank.estimators.GPCCA.macrostates is the hard assignment,cellrank.estimators.GPCCA.macrostates_memberships (please check) is the soft assignment.

Marius1311 commented on 2023-06-13T15:31:04Z ----------------------------------------------------------------

you're right, that seems to be the case. adapted.

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michalk8 commented on 2023-06-13T01:10:39Z ----------------------------------------------------------------

Can we please remove the horizontal and vertical lines + fix the figure aspect ratio?

Marius1311 commented on 2023-06-13T15:46:12Z ----------------------------------------------------------------

I don't know how

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michalk8 commented on 2023-06-13T01:10:40Z ----------------------------------------------------------------

adata.obs['clusters'] -> {attr}adata.obs['clusters'] <anndata.AnnData.obs>.

{mod}pyGPCCA doesn't link to anything

for more infos -> for more information.

Marius1311 commented on 2023-06-13T15:47:47Z ----------------------------------------------------------------

done.

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michalk8 commented on 2023-06-13T01:10:40Z ----------------------------------------------------------------

When mentioning PETSc/SLEPc, would consider adding the conda install -c conda-forge petsc4py slepc4py

Please don't hardcode the link to installation instructions, use the proper {doc}.

Marius1311 commented on 2023-06-13T15:50:48Z ----------------------------------------------------------------

ok, done

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michalk8 commented on 2023-06-13T01:10:42Z ----------------------------------------------------------------

"we use the ... method to identify the terminal states."

Marius1311 commented on 2023-06-13T15:51:24Z ----------------------------------------------------------------

ok.

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michalk8 commented on 2023-06-13T01:10:43Z ----------------------------------------------------------------

continious -> continuous

Marius1311 commented on 2023-06-13T15:52:01Z ----------------------------------------------------------------

ok, done.

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michalk8 commented on 2023-06-13T01:10:44Z ----------------------------------------------------------------

Maybe mention higher intensity/saturation means higher certainty.

Marius1311 commented on 2023-06-13T15:54:18Z ----------------------------------------------------------------

done.

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michalk8 commented on 2023-06-13T01:10:45Z ----------------------------------------------------------------

states using the {meth}... method.

Marius1311 commented on 2023-06-13T15:55:41Z ----------------------------------------------------------------

done.

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michalk8 commented on 2023-06-13T01:10:46Z ----------------------------------------------------------------

"and can be inspected conveniently."

I'd have expected you should g.initial_states and g.terminal_states

Marius1311 commented on 2023-06-13T16:01:44Z ----------------------------------------------------------------

Ok, I added that.

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michalk8 commented on 2023-06-13T01:10:47Z ----------------------------------------------------------------

inintial -> initial

Marius1311 commented on 2023-06-13T16:02:45Z ----------------------------------------------------------------

thanks.

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michalk8 commented on 2023-06-13T01:10:48Z ----------------------------------------------------------------

initial- -> initial

Marius1311 commented on 2023-06-13T16:03:01Z ----------------------------------------------------------------

done.

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michalk8 commented on 2023-06-13T01:10:49Z ----------------------------------------------------------------

Would not use italics for terminal.

knowlege -> knowledge

which we show below -> as shown below.

Marius1311 commented on 2023-06-13T16:03:44Z ----------------------------------------------------------------

ok.

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michalk8 commented on 2023-06-13T01:10:50Z ----------------------------------------------------------------

probabilits -> probability

Marius1311 commented on 2023-06-13T16:04:09Z ----------------------------------------------------------------

done.

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michalk8 commented on 2023-06-13T01:10:51Z ----------------------------------------------------------------

we compute the macrostates.

dashed vertical line

Marius1311 commented on 2023-06-13T16:04:49Z ----------------------------------------------------------------

ok.

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michalk8 commented on 2023-06-13T01:10:52Z ----------------------------------------------------------------

Remove the Nice!

...; however, that does -> . However, that does not

Missing . in the last sentence.

; we show below -> . We show below

" for each of the cells most confidently assigned to a certain macrostates" reads not so easily

Marius1311 commented on 2023-06-13T16:06:30Z ----------------------------------------------------------------

thanks, done

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michalk8 commented on 2023-06-13T01:10:53Z ----------------------------------------------------------------

any {attr}... -> any observation-level covariate

Link to the transport map kernel tutorial rather than the class (or both) (also missing the {class} role for the kernel).

Marius1311 commented on 2023-06-13T16:09:29Z ----------------------------------------------------------------

done.

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michalk8 commented on 2023-06-13T01:10:54Z ----------------------------------------------------------------

becasue -> because

Let's try the automatic terminal

Marius1311 commented on 2023-06-13T16:10:54Z ----------------------------------------------------------------

done.

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michalk8 commented on 2023-06-13T01:10:54Z ----------------------------------------------------------------

ductal-cell markers -> Ductal cell markers.

Marius1311 commented on 2023-06-13T16:11:44Z ----------------------------------------------------------------

done.

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michalk8 commented on 2023-06-13T01:10:55Z ----------------------------------------------------------------

as initial -> as an initial state.

Marius1311 commented on 2023-06-13T16:12:02Z ----------------------------------------------------------------

ok.

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michalk8 commented on 2023-06-13T01:10:56Z ----------------------------------------------------------------

we recommend... -> we recommend to: + go thrgouh/take a look/take a look/

Marius1311 commented on 2023-06-13T16:12:46Z ----------------------------------------------------------------

thanks!

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michalk8 commented on 2023-06-13T01:15:06Z ----------------------------------------------------------------

{attr) -> {attr}

Marius1311 commented on 2023-06-13T16:10:10Z ----------------------------------------------------------------

done.

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michalk8 commented on 2023-06-13T01:15:07Z ----------------------------------------------------------------

compute the {attr}fate probabilities <...> .

Marius1311 commented on 2023-06-13T16:11:19Z ----------------------------------------------------------------

done.

Marius1311 commented 1 year ago

makes sense. I moved it.

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Marius1311 commented 1 year ago

yes, I'll change this everywhere.

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Marius1311 commented 1 year ago

ok.

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Marius1311 commented 1 year ago

done.

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Marius1311 commented 1 year ago

I moved it to the first paragraph.

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Marius1311 commented 1 year ago

ok, adapted.

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Marius1311 commented 1 year ago

done, thanks!

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Marius1311 commented 1 year ago

ok.

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Marius1311 commented 1 year ago

well...

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Marius1311 commented 1 year ago

ok, done.

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Marius1311 commented 1 year ago

I removed these from the section heading.

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Marius1311 commented 1 year ago

included already (reuter:22)

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Marius1311 commented 1 year ago

you're right, that seems to be the case. adapted.

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michalk8 commented on 2023-06-13T01:10:27Z ----------------------------------------------------------------

Headings are too high, should be lower than Computing initial and terminal states

This holds also in the CytoTRACE tutorial and the Pseudotime tutorial.

Marius1311 commented on 2023-06-13T14:19:11Z ----------------------------------------------------------------

yes, I'll change this everywhere.

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michalk8 commented on 2023-06-13T01:10:28Z ----------------------------------------------------------------

The sentence "This tutorial does not depend" is too long, would split at "you may"

Would also rephrase (from negative to positive) and mention that this tutorial works with every other kernel + highlight this in bold.

Marius1311 commented on 2023-06-13T14:24:54Z ----------------------------------------------------------------

ok.

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michalk8 commented on 2023-06-13T01:10:29Z ----------------------------------------------------------------

you will need... -> you will need:

Please link to the other tutorials when mentioning the other kernels

Marius1311 commented on 2023-06-13T14:29:15Z ----------------------------------------------------------------

done.

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michalk8 commented on 2023-06-13T01:10:30Z ----------------------------------------------------------------

Would move to the note where you discuss the scverse forum.

Marius1311 commented on 2023-06-13T14:29:38Z ----------------------------------------------------------------

I moved it to the first paragraph.

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michalk8 commented on 2023-06-13T01:10:31Z ----------------------------------------------------------------

Line #4.    from scipy.stats import ttest_ind

Would slighly prefer import scipy.stats as st

_Marius1311 commented on 2023-06-13T15:15:34Z_ ----------------------------------------------------------------

ok, adapted.

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michalk8 commented on 2023-06-13T01:10:31Z ----------------------------------------------------------------

Use ~ when referring to anndata.AnnData.

"When you use a kernel to compute a transition matrix, this matrix, as well as a few informations about the computation, are written "

^ is not completely true, you have to call write_to_adata, maybe mention this.

Marius1311 commented on 2023-06-13T15:17:21Z ----------------------------------------------------------------

done, thanks!

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michalk8 commented on 2023-06-13T01:10:32Z ----------------------------------------------------------------

The {mod}~cellrank.estimators allowo you to analyze cell-state dynamics. We initialize the GPCCA estimator...

However, this and other estimators with with every CellRank {mod}kernel <cellrank.kernels>.

Marius1311 commented on 2023-06-13T15:19:53Z ----------------------------------------------------------------

ok.

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michalk8 commented on 2023-06-13T01:10:33Z ----------------------------------------------------------------

as we explain -> as explained

Marius1311 commented on 2023-06-13T15:20:53Z ----------------------------------------------------------------

well...

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michalk8 commented on 2023-06-13T01:10:34Z ----------------------------------------------------------------

"We'll demonstrate both modes in this tutorial."

There's a way to add links to section headers in myst, see, e.g., here: https://myst-parser.readthedocs.io/en/latest/syntax/cross-referencing.html#implicit-targets

{meth}schur decomposition-> {meth}Schur decomposition

Marius1311 commented on 2023-06-13T15:26:19Z ----------------------------------------------------------------

ok, done.

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michalk8 commented on 2023-06-13T01:10:35Z ----------------------------------------------------------------

Add links to fit() and predict() using the {meth} role.

Marius1311 commented on 2023-06-13T15:26:52Z ----------------------------------------------------------------

I removed these from the section heading.

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michalk8 commented on 2023-06-13T01:10:36Z ----------------------------------------------------------------

Two spaces in "algorithm as"

as implemented in the pyGPCCA package (cite the zenodo)

Marius1311 commented on 2023-06-13T15:27:43Z ----------------------------------------------------------------

included already (reuter:22)

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michalk8 commented on 2023-06-13T01:10:38Z ----------------------------------------------------------------

CellRank corases-grains -> CellRank coarse-grains.

If I remember correctly, cellrank.estimators.GPCCA.macrostates is the hard assignment,cellrank.estimators.GPCCA.macrostates_memberships (please check) is the soft assignment.

Marius1311 commented on 2023-06-13T15:31:04Z ----------------------------------------------------------------

you're right, that seems to be the case. adapted.

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michalk8 commented on 2023-06-13T01:10:39Z ----------------------------------------------------------------

Can we please remove the horizontal and vertical lines + fix the figure aspect ratio?

Marius1311 commented on 2023-06-13T15:46:12Z ----------------------------------------------------------------

I don't know how

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michalk8 commented on 2023-06-13T01:10:40Z ----------------------------------------------------------------

adata.obs['clusters'] -> {attr}adata.obs['clusters'] <anndata.AnnData.obs>.

{mod}pyGPCCA doesn't link to anything

for more infos -> for more information.

Marius1311 commented on 2023-06-13T15:47:47Z ----------------------------------------------------------------

done.

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michalk8 commented on 2023-06-13T01:10:40Z ----------------------------------------------------------------

When mentioning PETSc/SLEPc, would consider adding the conda install -c conda-forge petsc4py slepc4py

Please don't hardcode the link to installation instructions, use the proper {doc}.

Marius1311 commented on 2023-06-13T15:50:48Z ----------------------------------------------------------------

ok, done

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michalk8 commented on 2023-06-13T01:10:42Z ----------------------------------------------------------------

"we use the ... method to identify the terminal states."

Marius1311 commented on 2023-06-13T15:51:24Z ----------------------------------------------------------------

ok.

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michalk8 commented on 2023-06-13T01:10:43Z ----------------------------------------------------------------

continious -> continuous

Marius1311 commented on 2023-06-13T15:52:01Z ----------------------------------------------------------------

ok, done.

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michalk8 commented on 2023-06-13T01:10:44Z ----------------------------------------------------------------

Maybe mention higher intensity/saturation means higher certainty.

Marius1311 commented on 2023-06-13T15:54:18Z ----------------------------------------------------------------

done.

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michalk8 commented on 2023-06-13T01:10:45Z ----------------------------------------------------------------

states using the {meth}... method.

Marius1311 commented on 2023-06-13T15:55:41Z ----------------------------------------------------------------

done.

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michalk8 commented on 2023-06-13T01:10:46Z ----------------------------------------------------------------

"and can be inspected conveniently."

I'd have expected you should g.initial_states and g.terminal_states

Marius1311 commented on 2023-06-13T16:01:44Z ----------------------------------------------------------------

Ok, I added that.

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michalk8 commented on 2023-06-13T01:10:47Z ----------------------------------------------------------------

inintial -> initial

Marius1311 commented on 2023-06-13T16:02:45Z ----------------------------------------------------------------

thanks.

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michalk8 commented on 2023-06-13T01:10:48Z ----------------------------------------------------------------

initial- -> initial

Marius1311 commented on 2023-06-13T16:03:01Z ----------------------------------------------------------------

done.

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michalk8 commented on 2023-06-13T01:10:49Z ----------------------------------------------------------------

Would not use italics for terminal.

knowlege -> knowledge

which we show below -> as shown below.

Marius1311 commented on 2023-06-13T16:03:44Z ----------------------------------------------------------------

ok.

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michalk8 commented on 2023-06-13T01:10:50Z ----------------------------------------------------------------

probabilits -> probability

Marius1311 commented on 2023-06-13T16:04:09Z ----------------------------------------------------------------

done.

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michalk8 commented on 2023-06-13T01:10:51Z ----------------------------------------------------------------

we compute the macrostates.

dashed vertical line

Marius1311 commented on 2023-06-13T16:04:49Z ----------------------------------------------------------------

ok.

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michalk8 commented on 2023-06-13T01:10:52Z ----------------------------------------------------------------

Remove the Nice!

...; however, that does -> . However, that does not

Missing . in the last sentence.

; we show below -> . We show below

" for each of the cells most confidently assigned to a certain macrostates" reads not so easily

Marius1311 commented on 2023-06-13T16:06:30Z ----------------------------------------------------------------

thanks, done

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michalk8 commented on 2023-06-13T01:10:53Z ----------------------------------------------------------------

any {attr}... -> any observation-level covariate

Link to the transport map kernel tutorial rather than the class (or both) (also missing the {class} role for the kernel).

Marius1311 commented on 2023-06-13T16:09:29Z ----------------------------------------------------------------

done.

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michalk8 commented on 2023-06-13T01:10:54Z ----------------------------------------------------------------

becasue -> because

Let's try the automatic terminal

Marius1311 commented on 2023-06-13T16:10:54Z ----------------------------------------------------------------

done.

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michalk8 commented on 2023-06-13T01:10:54Z ----------------------------------------------------------------

ductal-cell markers -> Ductal cell markers.

Marius1311 commented on 2023-06-13T16:11:44Z ----------------------------------------------------------------

done.

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michalk8 commented on 2023-06-13T01:10:55Z ----------------------------------------------------------------

as initial -> as an initial state.

Marius1311 commented on 2023-06-13T16:12:02Z ----------------------------------------------------------------

ok.

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michalk8 commented on 2023-06-13T01:10:56Z ----------------------------------------------------------------

we recommend... -> we recommend to: + go thrgouh/take a look/take a look/

Marius1311 commented on 2023-06-13T16:12:46Z ----------------------------------------------------------------

thanks!

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michalk8 commented on 2023-06-13T01:15:06Z ----------------------------------------------------------------

{attr) -> {attr}

Marius1311 commented on 2023-06-13T16:10:10Z ----------------------------------------------------------------

done.

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michalk8 commented on 2023-06-13T01:15:07Z ----------------------------------------------------------------

compute the {attr}fate probabilities <...> .

Marius1311 commented on 2023-06-13T16:11:19Z ----------------------------------------------------------------

done.

Marius1311 commented 1 year ago

makes sense. I moved it.

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Marius1311 commented 1 year ago

yes, I'll change this everywhere.

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Marius1311 commented 1 year ago

ok.

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Marius1311 commented 1 year ago

done.

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Marius1311 commented 1 year ago

I moved it to the first paragraph.

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Marius1311 commented 1 year ago

ok, adapted.

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Marius1311 commented 1 year ago

done, thanks!

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Marius1311 commented 1 year ago

ok.

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Marius1311 commented 1 year ago

well...

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Marius1311 commented 1 year ago

ok, done.

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Marius1311 commented 1 year ago

I removed these from the section heading.

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Marius1311 commented 1 year ago

included already (reuter:22)

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Marius1311 commented 1 year ago

you're right, that seems to be the case. adapted.

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michalk8 commented on 2023-06-13T01:10:28Z ----------------------------------------------------------------

The sentence "This tutorial does not depend" is too long, would split at "you may"

Would also rephrase (from negative to positive) and mention that this tutorial works with every other kernel + highlight this in bold.

Marius1311 commented on 2023-06-13T14:24:54Z ----------------------------------------------------------------

ok.

review-notebook-app[bot] commented 1 year ago

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michalk8 commented on 2023-06-13T01:10:29Z ----------------------------------------------------------------

you will need... -> you will need:

Please link to the other tutorials when mentioning the other kernels

Marius1311 commented on 2023-06-13T14:29:15Z ----------------------------------------------------------------

done.

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michalk8 commented on 2023-06-13T01:10:30Z ----------------------------------------------------------------

Would move to the note where you discuss the scverse forum.

Marius1311 commented on 2023-06-13T14:29:38Z ----------------------------------------------------------------

I moved it to the first paragraph.

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michalk8 commented on 2023-06-13T01:10:31Z ----------------------------------------------------------------

Line #4.    from scipy.stats import ttest_ind

Would slighly prefer import scipy.stats as st

_Marius1311 commented on 2023-06-13T15:15:34Z_ ----------------------------------------------------------------

ok, adapted.

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michalk8 commented on 2023-06-13T01:10:31Z ----------------------------------------------------------------

Use ~ when referring to anndata.AnnData.

"When you use a kernel to compute a transition matrix, this matrix, as well as a few informations about the computation, are written "

^ is not completely true, you have to call write_to_adata, maybe mention this.

Marius1311 commented on 2023-06-13T15:17:21Z ----------------------------------------------------------------

done, thanks!

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michalk8 commented on 2023-06-13T01:10:32Z ----------------------------------------------------------------

The {mod}~cellrank.estimators allowo you to analyze cell-state dynamics. We initialize the GPCCA estimator...

However, this and other estimators with with every CellRank {mod}kernel <cellrank.kernels>.

Marius1311 commented on 2023-06-13T15:19:53Z ----------------------------------------------------------------

ok.

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michalk8 commented on 2023-06-13T01:10:33Z ----------------------------------------------------------------

as we explain -> as explained

Marius1311 commented on 2023-06-13T15:20:53Z ----------------------------------------------------------------

well...

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michalk8 commented on 2023-06-13T01:10:34Z ----------------------------------------------------------------

"We'll demonstrate both modes in this tutorial."

There's a way to add links to section headers in myst, see, e.g., here: https://myst-parser.readthedocs.io/en/latest/syntax/cross-referencing.html#implicit-targets

{meth}schur decomposition-> {meth}Schur decomposition

Marius1311 commented on 2023-06-13T15:26:19Z ----------------------------------------------------------------

ok, done.

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michalk8 commented on 2023-06-13T01:10:35Z ----------------------------------------------------------------

Add links to fit() and predict() using the {meth} role.

Marius1311 commented on 2023-06-13T15:26:52Z ----------------------------------------------------------------

I removed these from the section heading.

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michalk8 commented on 2023-06-13T01:10:36Z ----------------------------------------------------------------

Two spaces in "algorithm as"

as implemented in the pyGPCCA package (cite the zenodo)

Marius1311 commented on 2023-06-13T15:27:43Z ----------------------------------------------------------------

included already (reuter:22)

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michalk8 commented on 2023-06-13T01:10:38Z ----------------------------------------------------------------

CellRank corases-grains -> CellRank coarse-grains.

If I remember correctly, cellrank.estimators.GPCCA.macrostates is the hard assignment,cellrank.estimators.GPCCA.macrostates_memberships (please check) is the soft assignment.

Marius1311 commented on 2023-06-13T15:31:04Z ----------------------------------------------------------------

you're right, that seems to be the case. adapted.

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michalk8 commented on 2023-06-13T01:10:39Z ----------------------------------------------------------------

Can we please remove the horizontal and vertical lines + fix the figure aspect ratio?

Marius1311 commented on 2023-06-13T15:46:12Z ----------------------------------------------------------------

I don't know how

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michalk8 commented on 2023-06-13T01:10:40Z ----------------------------------------------------------------

adata.obs['clusters'] -> {attr}adata.obs['clusters'] <anndata.AnnData.obs>.

{mod}pyGPCCA doesn't link to anything

for more infos -> for more information.

Marius1311 commented on 2023-06-13T15:47:47Z ----------------------------------------------------------------

done.

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michalk8 commented on 2023-06-13T01:10:40Z ----------------------------------------------------------------

When mentioning PETSc/SLEPc, would consider adding the conda install -c conda-forge petsc4py slepc4py

Please don't hardcode the link to installation instructions, use the proper {doc}.

Marius1311 commented on 2023-06-13T15:50:48Z ----------------------------------------------------------------

ok, done

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michalk8 commented on 2023-06-13T01:10:42Z ----------------------------------------------------------------

"we use the ... method to identify the terminal states."

Marius1311 commented on 2023-06-13T15:51:24Z ----------------------------------------------------------------

ok.

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michalk8 commented on 2023-06-13T01:10:43Z ----------------------------------------------------------------

continious -> continuous

Marius1311 commented on 2023-06-13T15:52:01Z ----------------------------------------------------------------

ok, done.

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michalk8 commented on 2023-06-13T01:10:44Z ----------------------------------------------------------------

Maybe mention higher intensity/saturation means higher certainty.

Marius1311 commented on 2023-06-13T15:54:18Z ----------------------------------------------------------------

done.

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michalk8 commented on 2023-06-13T01:10:45Z ----------------------------------------------------------------

states using the {meth}... method.

Marius1311 commented on 2023-06-13T15:55:41Z ----------------------------------------------------------------

done.

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michalk8 commented on 2023-06-13T01:10:46Z ----------------------------------------------------------------

"and can be inspected conveniently."

I'd have expected you should g.initial_states and g.terminal_states

Marius1311 commented on 2023-06-13T16:01:44Z ----------------------------------------------------------------

Ok, I added that.

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michalk8 commented on 2023-06-13T01:10:47Z ----------------------------------------------------------------

inintial -> initial

Marius1311 commented on 2023-06-13T16:02:45Z ----------------------------------------------------------------

thanks.

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michalk8 commented on 2023-06-13T01:10:48Z ----------------------------------------------------------------

initial- -> initial

Marius1311 commented on 2023-06-13T16:03:01Z ----------------------------------------------------------------

done.

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michalk8 commented on 2023-06-13T01:10:49Z ----------------------------------------------------------------

Would not use italics for terminal.

knowlege -> knowledge

which we show below -> as shown below.

Marius1311 commented on 2023-06-13T16:03:44Z ----------------------------------------------------------------

ok.

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michalk8 commented on 2023-06-13T01:10:50Z ----------------------------------------------------------------

probabilits -> probability

Marius1311 commented on 2023-06-13T16:04:09Z ----------------------------------------------------------------

done.

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michalk8 commented on 2023-06-13T01:10:51Z ----------------------------------------------------------------

we compute the macrostates.

dashed vertical line

Marius1311 commented on 2023-06-13T16:04:49Z ----------------------------------------------------------------

ok.

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michalk8 commented on 2023-06-13T01:10:52Z ----------------------------------------------------------------

Remove the Nice!

...; however, that does -> . However, that does not

Missing . in the last sentence.

; we show below -> . We show below

" for each of the cells most confidently assigned to a certain macrostates" reads not so easily

Marius1311 commented on 2023-06-13T16:06:30Z ----------------------------------------------------------------

thanks, done

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michalk8 commented on 2023-06-13T01:10:53Z ----------------------------------------------------------------

any {attr}... -> any observation-level covariate

Link to the transport map kernel tutorial rather than the class (or both) (also missing the {class} role for the kernel).

Marius1311 commented on 2023-06-13T16:09:29Z ----------------------------------------------------------------

done.

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michalk8 commented on 2023-06-13T01:10:54Z ----------------------------------------------------------------

becasue -> because

Let's try the automatic terminal

Marius1311 commented on 2023-06-13T16:10:54Z ----------------------------------------------------------------

done.

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michalk8 commented on 2023-06-13T01:10:54Z ----------------------------------------------------------------

ductal-cell markers -> Ductal cell markers.

Marius1311 commented on 2023-06-13T16:11:44Z ----------------------------------------------------------------

done.

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michalk8 commented on 2023-06-13T01:10:55Z ----------------------------------------------------------------

as initial -> as an initial state.

Marius1311 commented on 2023-06-13T16:12:02Z ----------------------------------------------------------------

ok.

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michalk8 commented on 2023-06-13T01:10:56Z ----------------------------------------------------------------

we recommend... -> we recommend to: + go thrgouh/take a look/take a look/

Marius1311 commented on 2023-06-13T16:12:46Z ----------------------------------------------------------------

thanks!

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michalk8 commented on 2023-06-13T01:15:06Z ----------------------------------------------------------------

{attr) -> {attr}

Marius1311 commented on 2023-06-13T16:10:10Z ----------------------------------------------------------------

done.

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michalk8 commented on 2023-06-13T01:15:07Z ----------------------------------------------------------------

compute the {attr}fate probabilities <...> .

Marius1311 commented on 2023-06-13T16:11:19Z ----------------------------------------------------------------

done.

Marius1311 commented 1 year ago

makes sense. I moved it.

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Marius1311 commented 1 year ago

yes, I'll change this everywhere.

---

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Marius1311 commented 1 year ago

ok.

---

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Marius1311 commented 1 year ago

done.

---

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Marius1311 commented 1 year ago

I moved it to the first paragraph.

---

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Marius1311 commented 1 year ago

ok, adapted.

---

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Marius1311 commented 1 year ago

done, thanks!

---

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Marius1311 commented 1 year ago

ok.

---

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Marius1311 commented 1 year ago

well...

---

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Marius1311 commented 1 year ago

ok, done.

---

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Marius1311 commented 1 year ago

I removed these from the section heading.

---

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Marius1311 commented 1 year ago

included already (reuter:22)

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Marius1311 commented 1 year ago

you're right, that seems to be the case. adapted.

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michalk8 commented on 2023-06-13T01:10:29Z ----------------------------------------------------------------

you will need... -> you will need:

Please link to the other tutorials when mentioning the other kernels

Marius1311 commented on 2023-06-13T14:29:15Z ----------------------------------------------------------------

done.

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michalk8 commented on 2023-06-13T01:10:30Z ----------------------------------------------------------------

Would move to the note where you discuss the scverse forum.

Marius1311 commented on 2023-06-13T14:29:38Z ----------------------------------------------------------------

I moved it to the first paragraph.

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michalk8 commented on 2023-06-13T01:10:31Z ----------------------------------------------------------------

Line #4.    from scipy.stats import ttest_ind

Would slighly prefer import scipy.stats as st

_Marius1311 commented on 2023-06-13T15:15:34Z_ ----------------------------------------------------------------

ok, adapted.

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michalk8 commented on 2023-06-13T01:10:31Z ----------------------------------------------------------------

Use ~ when referring to anndata.AnnData.

"When you use a kernel to compute a transition matrix, this matrix, as well as a few informations about the computation, are written "

^ is not completely true, you have to call write_to_adata, maybe mention this.

Marius1311 commented on 2023-06-13T15:17:21Z ----------------------------------------------------------------

done, thanks!

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michalk8 commented on 2023-06-13T01:10:32Z ----------------------------------------------------------------

The {mod}~cellrank.estimators allowo you to analyze cell-state dynamics. We initialize the GPCCA estimator...

However, this and other estimators with with every CellRank {mod}kernel <cellrank.kernels>.

Marius1311 commented on 2023-06-13T15:19:53Z ----------------------------------------------------------------

ok.

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michalk8 commented on 2023-06-13T01:10:33Z ----------------------------------------------------------------

as we explain -> as explained

Marius1311 commented on 2023-06-13T15:20:53Z ----------------------------------------------------------------

well...

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michalk8 commented on 2023-06-13T01:10:34Z ----------------------------------------------------------------

"We'll demonstrate both modes in this tutorial."

There's a way to add links to section headers in myst, see, e.g., here: https://myst-parser.readthedocs.io/en/latest/syntax/cross-referencing.html#implicit-targets

{meth}schur decomposition-> {meth}Schur decomposition

Marius1311 commented on 2023-06-13T15:26:19Z ----------------------------------------------------------------

ok, done.

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michalk8 commented on 2023-06-13T01:10:35Z ----------------------------------------------------------------

Add links to fit() and predict() using the {meth} role.

Marius1311 commented on 2023-06-13T15:26:52Z ----------------------------------------------------------------

I removed these from the section heading.

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michalk8 commented on 2023-06-13T01:10:36Z ----------------------------------------------------------------

Two spaces in "algorithm as"

as implemented in the pyGPCCA package (cite the zenodo)

Marius1311 commented on 2023-06-13T15:27:43Z ----------------------------------------------------------------

included already (reuter:22)

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michalk8 commented on 2023-06-13T01:10:38Z ----------------------------------------------------------------

CellRank corases-grains -> CellRank coarse-grains.

If I remember correctly, cellrank.estimators.GPCCA.macrostates is the hard assignment,cellrank.estimators.GPCCA.macrostates_memberships (please check) is the soft assignment.

Marius1311 commented on 2023-06-13T15:31:04Z ----------------------------------------------------------------

you're right, that seems to be the case. adapted.

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michalk8 commented on 2023-06-13T01:10:39Z ----------------------------------------------------------------

Can we please remove the horizontal and vertical lines + fix the figure aspect ratio?

Marius1311 commented on 2023-06-13T15:46:12Z ----------------------------------------------------------------

I don't know how

review-notebook-app[bot] commented 1 year ago

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michalk8 commented on 2023-06-13T01:10:40Z ----------------------------------------------------------------

adata.obs['clusters'] -> {attr}adata.obs['clusters'] <anndata.AnnData.obs>.

{mod}pyGPCCA doesn't link to anything

for more infos -> for more information.

Marius1311 commented on 2023-06-13T15:47:47Z ----------------------------------------------------------------

done.

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michalk8 commented on 2023-06-13T01:10:40Z ----------------------------------------------------------------

When mentioning PETSc/SLEPc, would consider adding the conda install -c conda-forge petsc4py slepc4py

Please don't hardcode the link to installation instructions, use the proper {doc}.

Marius1311 commented on 2023-06-13T15:50:48Z ----------------------------------------------------------------

ok, done

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michalk8 commented on 2023-06-13T01:10:42Z ----------------------------------------------------------------

"we use the ... method to identify the terminal states."

Marius1311 commented on 2023-06-13T15:51:24Z ----------------------------------------------------------------

ok.

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michalk8 commented on 2023-06-13T01:10:43Z ----------------------------------------------------------------

continious -> continuous

Marius1311 commented on 2023-06-13T15:52:01Z ----------------------------------------------------------------

ok, done.

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michalk8 commented on 2023-06-13T01:10:44Z ----------------------------------------------------------------

Maybe mention higher intensity/saturation means higher certainty.

Marius1311 commented on 2023-06-13T15:54:18Z ----------------------------------------------------------------

done.

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michalk8 commented on 2023-06-13T01:10:45Z ----------------------------------------------------------------

states using the {meth}... method.

Marius1311 commented on 2023-06-13T15:55:41Z ----------------------------------------------------------------

done.

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michalk8 commented on 2023-06-13T01:10:46Z ----------------------------------------------------------------

"and can be inspected conveniently."

I'd have expected you should g.initial_states and g.terminal_states

Marius1311 commented on 2023-06-13T16:01:44Z ----------------------------------------------------------------

Ok, I added that.

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michalk8 commented on 2023-06-13T01:10:47Z ----------------------------------------------------------------

inintial -> initial

Marius1311 commented on 2023-06-13T16:02:45Z ----------------------------------------------------------------

thanks.

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michalk8 commented on 2023-06-13T01:10:48Z ----------------------------------------------------------------

initial- -> initial

Marius1311 commented on 2023-06-13T16:03:01Z ----------------------------------------------------------------

done.

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michalk8 commented on 2023-06-13T01:10:49Z ----------------------------------------------------------------

Would not use italics for terminal.

knowlege -> knowledge

which we show below -> as shown below.

Marius1311 commented on 2023-06-13T16:03:44Z ----------------------------------------------------------------

ok.

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michalk8 commented on 2023-06-13T01:10:50Z ----------------------------------------------------------------

probabilits -> probability

Marius1311 commented on 2023-06-13T16:04:09Z ----------------------------------------------------------------

done.

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michalk8 commented on 2023-06-13T01:10:51Z ----------------------------------------------------------------

we compute the macrostates.

dashed vertical line

Marius1311 commented on 2023-06-13T16:04:49Z ----------------------------------------------------------------

ok.

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michalk8 commented on 2023-06-13T01:10:52Z ----------------------------------------------------------------

Remove the Nice!

...; however, that does -> . However, that does not

Missing . in the last sentence.

; we show below -> . We show below

" for each of the cells most confidently assigned to a certain macrostates" reads not so easily

Marius1311 commented on 2023-06-13T16:06:30Z ----------------------------------------------------------------

thanks, done

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michalk8 commented on 2023-06-13T01:10:53Z ----------------------------------------------------------------

any {attr}... -> any observation-level covariate

Link to the transport map kernel tutorial rather than the class (or both) (also missing the {class} role for the kernel).

Marius1311 commented on 2023-06-13T16:09:29Z ----------------------------------------------------------------

done.

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michalk8 commented on 2023-06-13T01:10:54Z ----------------------------------------------------------------

becasue -> because

Let's try the automatic terminal

Marius1311 commented on 2023-06-13T16:10:54Z ----------------------------------------------------------------

done.

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michalk8 commented on 2023-06-13T01:10:54Z ----------------------------------------------------------------

ductal-cell markers -> Ductal cell markers.

Marius1311 commented on 2023-06-13T16:11:44Z ----------------------------------------------------------------

done.

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michalk8 commented on 2023-06-13T01:10:55Z ----------------------------------------------------------------

as initial -> as an initial state.

Marius1311 commented on 2023-06-13T16:12:02Z ----------------------------------------------------------------

ok.

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michalk8 commented on 2023-06-13T01:10:56Z ----------------------------------------------------------------

we recommend... -> we recommend to: + go thrgouh/take a look/take a look/

Marius1311 commented on 2023-06-13T16:12:46Z ----------------------------------------------------------------

thanks!

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michalk8 commented on 2023-06-13T01:15:06Z ----------------------------------------------------------------

{attr) -> {attr}

Marius1311 commented on 2023-06-13T16:10:10Z ----------------------------------------------------------------

done.

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michalk8 commented on 2023-06-13T01:15:07Z ----------------------------------------------------------------

compute the {attr}fate probabilities <...> .

Marius1311 commented on 2023-06-13T16:11:19Z ----------------------------------------------------------------

done.

Marius1311 commented 1 year ago

makes sense. I moved it.

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Marius1311 commented 1 year ago

yes, I'll change this everywhere.

---

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Marius1311 commented 1 year ago

ok.

---

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Marius1311 commented 1 year ago

done.

---

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Marius1311 commented 1 year ago

I moved it to the first paragraph.

---

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Marius1311 commented 1 year ago

ok, adapted.

---

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Marius1311 commented 1 year ago

done, thanks!

---

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Marius1311 commented 1 year ago

ok.

---

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Marius1311 commented 1 year ago

well...

---

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Marius1311 commented 1 year ago

ok, done.

---

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Marius1311 commented 1 year ago

I removed these from the section heading.

---

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Marius1311 commented 1 year ago

included already (reuter:22)

---

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Marius1311 commented 1 year ago

you're right, that seems to be the case. adapted.

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michalk8 commented on 2023-06-13T01:10:30Z ----------------------------------------------------------------

Would move to the note where you discuss the scverse forum.

Marius1311 commented on 2023-06-13T14:29:38Z ----------------------------------------------------------------

I moved it to the first paragraph.

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michalk8 commented on 2023-06-13T01:10:31Z ----------------------------------------------------------------

Line #4.    from scipy.stats import ttest_ind

Would slighly prefer import scipy.stats as st

_Marius1311 commented on 2023-06-13T15:15:34Z_ ----------------------------------------------------------------

ok, adapted.

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michalk8 commented on 2023-06-13T01:10:31Z ----------------------------------------------------------------

Use ~ when referring to anndata.AnnData.

"When you use a kernel to compute a transition matrix, this matrix, as well as a few informations about the computation, are written "

^ is not completely true, you have to call write_to_adata, maybe mention this.

Marius1311 commented on 2023-06-13T15:17:21Z ----------------------------------------------------------------

done, thanks!

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michalk8 commented on 2023-06-13T01:10:32Z ----------------------------------------------------------------

The {mod}~cellrank.estimators allowo you to analyze cell-state dynamics. We initialize the GPCCA estimator...

However, this and other estimators with with every CellRank {mod}kernel <cellrank.kernels>.

Marius1311 commented on 2023-06-13T15:19:53Z ----------------------------------------------------------------

ok.

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michalk8 commented on 2023-06-13T01:10:33Z ----------------------------------------------------------------

as we explain -> as explained

Marius1311 commented on 2023-06-13T15:20:53Z ----------------------------------------------------------------

well...

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michalk8 commented on 2023-06-13T01:10:34Z ----------------------------------------------------------------

"We'll demonstrate both modes in this tutorial."

There's a way to add links to section headers in myst, see, e.g., here: https://myst-parser.readthedocs.io/en/latest/syntax/cross-referencing.html#implicit-targets

{meth}schur decomposition-> {meth}Schur decomposition

Marius1311 commented on 2023-06-13T15:26:19Z ----------------------------------------------------------------

ok, done.

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michalk8 commented on 2023-06-13T01:10:35Z ----------------------------------------------------------------

Add links to fit() and predict() using the {meth} role.

Marius1311 commented on 2023-06-13T15:26:52Z ----------------------------------------------------------------

I removed these from the section heading.

review-notebook-app[bot] commented 1 year ago

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michalk8 commented on 2023-06-13T01:10:36Z ----------------------------------------------------------------

Two spaces in "algorithm as"

as implemented in the pyGPCCA package (cite the zenodo)

Marius1311 commented on 2023-06-13T15:27:43Z ----------------------------------------------------------------

included already (reuter:22)

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michalk8 commented on 2023-06-13T01:10:38Z ----------------------------------------------------------------

CellRank corases-grains -> CellRank coarse-grains.

If I remember correctly, cellrank.estimators.GPCCA.macrostates is the hard assignment,cellrank.estimators.GPCCA.macrostates_memberships (please check) is the soft assignment.

Marius1311 commented on 2023-06-13T15:31:04Z ----------------------------------------------------------------

you're right, that seems to be the case. adapted.

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michalk8 commented on 2023-06-13T01:10:39Z ----------------------------------------------------------------

Can we please remove the horizontal and vertical lines + fix the figure aspect ratio?

Marius1311 commented on 2023-06-13T15:46:12Z ----------------------------------------------------------------

I don't know how

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michalk8 commented on 2023-06-13T01:10:40Z ----------------------------------------------------------------

adata.obs['clusters'] -> {attr}adata.obs['clusters'] <anndata.AnnData.obs>.

{mod}pyGPCCA doesn't link to anything

for more infos -> for more information.

Marius1311 commented on 2023-06-13T15:47:47Z ----------------------------------------------------------------

done.

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michalk8 commented on 2023-06-13T01:10:40Z ----------------------------------------------------------------

When mentioning PETSc/SLEPc, would consider adding the conda install -c conda-forge petsc4py slepc4py

Please don't hardcode the link to installation instructions, use the proper {doc}.

Marius1311 commented on 2023-06-13T15:50:48Z ----------------------------------------------------------------

ok, done

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michalk8 commented on 2023-06-13T01:10:42Z ----------------------------------------------------------------

"we use the ... method to identify the terminal states."

Marius1311 commented on 2023-06-13T15:51:24Z ----------------------------------------------------------------

ok.

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michalk8 commented on 2023-06-13T01:10:43Z ----------------------------------------------------------------

continious -> continuous

Marius1311 commented on 2023-06-13T15:52:01Z ----------------------------------------------------------------

ok, done.

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michalk8 commented on 2023-06-13T01:10:44Z ----------------------------------------------------------------

Maybe mention higher intensity/saturation means higher certainty.

Marius1311 commented on 2023-06-13T15:54:18Z ----------------------------------------------------------------

done.

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michalk8 commented on 2023-06-13T01:10:45Z ----------------------------------------------------------------

states using the {meth}... method.

Marius1311 commented on 2023-06-13T15:55:41Z ----------------------------------------------------------------

done.

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michalk8 commented on 2023-06-13T01:10:46Z ----------------------------------------------------------------

"and can be inspected conveniently."

I'd have expected you should g.initial_states and g.terminal_states

Marius1311 commented on 2023-06-13T16:01:44Z ----------------------------------------------------------------

Ok, I added that.

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michalk8 commented on 2023-06-13T01:10:47Z ----------------------------------------------------------------

inintial -> initial

Marius1311 commented on 2023-06-13T16:02:45Z ----------------------------------------------------------------

thanks.

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michalk8 commented on 2023-06-13T01:10:48Z ----------------------------------------------------------------

initial- -> initial

Marius1311 commented on 2023-06-13T16:03:01Z ----------------------------------------------------------------

done.

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michalk8 commented on 2023-06-13T01:10:49Z ----------------------------------------------------------------

Would not use italics for terminal.

knowlege -> knowledge

which we show below -> as shown below.

Marius1311 commented on 2023-06-13T16:03:44Z ----------------------------------------------------------------

ok.

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michalk8 commented on 2023-06-13T01:10:50Z ----------------------------------------------------------------

probabilits -> probability

Marius1311 commented on 2023-06-13T16:04:09Z ----------------------------------------------------------------

done.

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michalk8 commented on 2023-06-13T01:10:51Z ----------------------------------------------------------------

we compute the macrostates.

dashed vertical line

Marius1311 commented on 2023-06-13T16:04:49Z ----------------------------------------------------------------

ok.

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michalk8 commented on 2023-06-13T01:10:52Z ----------------------------------------------------------------

Remove the Nice!

...; however, that does -> . However, that does not

Missing . in the last sentence.

; we show below -> . We show below

" for each of the cells most confidently assigned to a certain macrostates" reads not so easily

Marius1311 commented on 2023-06-13T16:06:30Z ----------------------------------------------------------------

thanks, done

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michalk8 commented on 2023-06-13T01:10:53Z ----------------------------------------------------------------

any {attr}... -> any observation-level covariate

Link to the transport map kernel tutorial rather than the class (or both) (also missing the {class} role for the kernel).

Marius1311 commented on 2023-06-13T16:09:29Z ----------------------------------------------------------------

done.

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michalk8 commented on 2023-06-13T01:10:54Z ----------------------------------------------------------------

becasue -> because

Let's try the automatic terminal

Marius1311 commented on 2023-06-13T16:10:54Z ----------------------------------------------------------------

done.

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michalk8 commented on 2023-06-13T01:10:54Z ----------------------------------------------------------------

ductal-cell markers -> Ductal cell markers.

Marius1311 commented on 2023-06-13T16:11:44Z ----------------------------------------------------------------

done.

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michalk8 commented on 2023-06-13T01:10:55Z ----------------------------------------------------------------

as initial -> as an initial state.

Marius1311 commented on 2023-06-13T16:12:02Z ----------------------------------------------------------------

ok.

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michalk8 commented on 2023-06-13T01:10:56Z ----------------------------------------------------------------

we recommend... -> we recommend to: + go thrgouh/take a look/take a look/

Marius1311 commented on 2023-06-13T16:12:46Z ----------------------------------------------------------------

thanks!

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michalk8 commented on 2023-06-13T01:15:06Z ----------------------------------------------------------------

{attr) -> {attr}

Marius1311 commented on 2023-06-13T16:10:10Z ----------------------------------------------------------------

done.

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michalk8 commented on 2023-06-13T01:15:07Z ----------------------------------------------------------------

compute the {attr}fate probabilities <...> .

Marius1311 commented on 2023-06-13T16:11:19Z ----------------------------------------------------------------

done.

Marius1311 commented 1 year ago

makes sense. I moved it.

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Marius1311 commented 1 year ago

yes, I'll change this everywhere.

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Marius1311 commented 1 year ago

ok.

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Marius1311 commented 1 year ago

done.

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Marius1311 commented 1 year ago

I moved it to the first paragraph.

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Marius1311 commented 1 year ago

ok, adapted.

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Marius1311 commented 1 year ago

done, thanks!

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Marius1311 commented 1 year ago

ok.

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Marius1311 commented 1 year ago

well...

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Marius1311 commented 1 year ago

ok, done.

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Marius1311 commented 1 year ago

I removed these from the section heading.

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Marius1311 commented 1 year ago

included already (reuter:22)

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Marius1311 commented 1 year ago

you're right, that seems to be the case. adapted.

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michalk8 commented on 2023-06-13T01:10:31Z ----------------------------------------------------------------

Line #4.    from scipy.stats import ttest_ind

Would slighly prefer import scipy.stats as st

_Marius1311 commented on 2023-06-13T15:15:34Z_ ----------------------------------------------------------------

ok, adapted.

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michalk8 commented on 2023-06-13T01:10:31Z ----------------------------------------------------------------

Use ~ when referring to anndata.AnnData.

"When you use a kernel to compute a transition matrix, this matrix, as well as a few informations about the computation, are written "

^ is not completely true, you have to call write_to_adata, maybe mention this.

Marius1311 commented on 2023-06-13T15:17:21Z ----------------------------------------------------------------

done, thanks!

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michalk8 commented on 2023-06-13T01:10:32Z ----------------------------------------------------------------

The {mod}~cellrank.estimators allowo you to analyze cell-state dynamics. We initialize the GPCCA estimator...

However, this and other estimators with with every CellRank {mod}kernel <cellrank.kernels>.

Marius1311 commented on 2023-06-13T15:19:53Z ----------------------------------------------------------------

ok.

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michalk8 commented on 2023-06-13T01:10:33Z ----------------------------------------------------------------

as we explain -> as explained

Marius1311 commented on 2023-06-13T15:20:53Z ----------------------------------------------------------------

well...

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michalk8 commented on 2023-06-13T01:10:34Z ----------------------------------------------------------------

"We'll demonstrate both modes in this tutorial."

There's a way to add links to section headers in myst, see, e.g., here: https://myst-parser.readthedocs.io/en/latest/syntax/cross-referencing.html#implicit-targets

{meth}schur decomposition-> {meth}Schur decomposition

Marius1311 commented on 2023-06-13T15:26:19Z ----------------------------------------------------------------

ok, done.

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michalk8 commented on 2023-06-13T01:10:35Z ----------------------------------------------------------------

Add links to fit() and predict() using the {meth} role.

Marius1311 commented on 2023-06-13T15:26:52Z ----------------------------------------------------------------

I removed these from the section heading.

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michalk8 commented on 2023-06-13T01:10:36Z ----------------------------------------------------------------

Two spaces in "algorithm as"

as implemented in the pyGPCCA package (cite the zenodo)

Marius1311 commented on 2023-06-13T15:27:43Z ----------------------------------------------------------------

included already (reuter:22)

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michalk8 commented on 2023-06-13T01:10:38Z ----------------------------------------------------------------

CellRank corases-grains -> CellRank coarse-grains.

If I remember correctly, cellrank.estimators.GPCCA.macrostates is the hard assignment,cellrank.estimators.GPCCA.macrostates_memberships (please check) is the soft assignment.

Marius1311 commented on 2023-06-13T15:31:04Z ----------------------------------------------------------------

you're right, that seems to be the case. adapted.

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michalk8 commented on 2023-06-13T01:10:39Z ----------------------------------------------------------------

Can we please remove the horizontal and vertical lines + fix the figure aspect ratio?

Marius1311 commented on 2023-06-13T15:46:12Z ----------------------------------------------------------------

I don't know how

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michalk8 commented on 2023-06-13T01:10:40Z ----------------------------------------------------------------

adata.obs['clusters'] -> {attr}adata.obs['clusters'] <anndata.AnnData.obs>.

{mod}pyGPCCA doesn't link to anything

for more infos -> for more information.

Marius1311 commented on 2023-06-13T15:47:47Z ----------------------------------------------------------------

done.

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michalk8 commented on 2023-06-13T01:10:40Z ----------------------------------------------------------------

When mentioning PETSc/SLEPc, would consider adding the conda install -c conda-forge petsc4py slepc4py

Please don't hardcode the link to installation instructions, use the proper {doc}.

Marius1311 commented on 2023-06-13T15:50:48Z ----------------------------------------------------------------

ok, done

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michalk8 commented on 2023-06-13T01:10:42Z ----------------------------------------------------------------

"we use the ... method to identify the terminal states."

Marius1311 commented on 2023-06-13T15:51:24Z ----------------------------------------------------------------

ok.

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michalk8 commented on 2023-06-13T01:10:43Z ----------------------------------------------------------------

continious -> continuous

Marius1311 commented on 2023-06-13T15:52:01Z ----------------------------------------------------------------

ok, done.

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michalk8 commented on 2023-06-13T01:10:44Z ----------------------------------------------------------------

Maybe mention higher intensity/saturation means higher certainty.

Marius1311 commented on 2023-06-13T15:54:18Z ----------------------------------------------------------------

done.

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michalk8 commented on 2023-06-13T01:10:45Z ----------------------------------------------------------------

states using the {meth}... method.

Marius1311 commented on 2023-06-13T15:55:41Z ----------------------------------------------------------------

done.

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michalk8 commented on 2023-06-13T01:10:46Z ----------------------------------------------------------------

"and can be inspected conveniently."

I'd have expected you should g.initial_states and g.terminal_states

Marius1311 commented on 2023-06-13T16:01:44Z ----------------------------------------------------------------

Ok, I added that.

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michalk8 commented on 2023-06-13T01:10:47Z ----------------------------------------------------------------

inintial -> initial

Marius1311 commented on 2023-06-13T16:02:45Z ----------------------------------------------------------------

thanks.

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michalk8 commented on 2023-06-13T01:10:48Z ----------------------------------------------------------------

initial- -> initial

Marius1311 commented on 2023-06-13T16:03:01Z ----------------------------------------------------------------

done.

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michalk8 commented on 2023-06-13T01:10:49Z ----------------------------------------------------------------

Would not use italics for terminal.

knowlege -> knowledge

which we show below -> as shown below.

Marius1311 commented on 2023-06-13T16:03:44Z ----------------------------------------------------------------

ok.

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michalk8 commented on 2023-06-13T01:10:50Z ----------------------------------------------------------------

probabilits -> probability

Marius1311 commented on 2023-06-13T16:04:09Z ----------------------------------------------------------------

done.

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michalk8 commented on 2023-06-13T01:10:51Z ----------------------------------------------------------------

we compute the macrostates.

dashed vertical line

Marius1311 commented on 2023-06-13T16:04:49Z ----------------------------------------------------------------

ok.

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michalk8 commented on 2023-06-13T01:10:52Z ----------------------------------------------------------------

Remove the Nice!

...; however, that does -> . However, that does not

Missing . in the last sentence.

; we show below -> . We show below

" for each of the cells most confidently assigned to a certain macrostates" reads not so easily

Marius1311 commented on 2023-06-13T16:06:30Z ----------------------------------------------------------------

thanks, done

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michalk8 commented on 2023-06-13T01:10:53Z ----------------------------------------------------------------

any {attr}... -> any observation-level covariate

Link to the transport map kernel tutorial rather than the class (or both) (also missing the {class} role for the kernel).

Marius1311 commented on 2023-06-13T16:09:29Z ----------------------------------------------------------------

done.

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michalk8 commented on 2023-06-13T01:10:54Z ----------------------------------------------------------------

becasue -> because

Let's try the automatic terminal

Marius1311 commented on 2023-06-13T16:10:54Z ----------------------------------------------------------------

done.

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michalk8 commented on 2023-06-13T01:10:54Z ----------------------------------------------------------------

ductal-cell markers -> Ductal cell markers.

Marius1311 commented on 2023-06-13T16:11:44Z ----------------------------------------------------------------

done.

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michalk8 commented on 2023-06-13T01:10:55Z ----------------------------------------------------------------

as initial -> as an initial state.

Marius1311 commented on 2023-06-13T16:12:02Z ----------------------------------------------------------------

ok.

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michalk8 commented on 2023-06-13T01:10:56Z ----------------------------------------------------------------

we recommend... -> we recommend to: + go thrgouh/take a look/take a look/

Marius1311 commented on 2023-06-13T16:12:46Z ----------------------------------------------------------------

thanks!

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michalk8 commented on 2023-06-13T01:15:06Z ----------------------------------------------------------------

{attr) -> {attr}

Marius1311 commented on 2023-06-13T16:10:10Z ----------------------------------------------------------------

done.

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michalk8 commented on 2023-06-13T01:15:07Z ----------------------------------------------------------------

compute the {attr}fate probabilities <...> .

Marius1311 commented on 2023-06-13T16:11:19Z ----------------------------------------------------------------

done.

Marius1311 commented 1 year ago

makes sense. I moved it.

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Marius1311 commented 1 year ago

yes, I'll change this everywhere.

---

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Marius1311 commented 1 year ago

ok.

---

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Marius1311 commented 1 year ago

done.

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Marius1311 commented 1 year ago

I moved it to the first paragraph.

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Marius1311 commented 1 year ago

ok, adapted.

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Marius1311 commented 1 year ago

done, thanks!

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Marius1311 commented 1 year ago

ok.

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Marius1311 commented 1 year ago

well...

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Marius1311 commented 1 year ago

ok, done.

---

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Marius1311 commented 1 year ago

I removed these from the section heading.

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Marius1311 commented 1 year ago

included already (reuter:22)

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you're right, that seems to be the case. adapted.

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michalk8 commented on 2023-06-13T01:10:31Z ----------------------------------------------------------------

Use ~ when referring to anndata.AnnData.

"When you use a kernel to compute a transition matrix, this matrix, as well as a few informations about the computation, are written "

^ is not completely true, you have to call write_to_adata, maybe mention this.

Marius1311 commented on 2023-06-13T15:17:21Z ----------------------------------------------------------------

done, thanks!

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michalk8 commented on 2023-06-13T01:10:32Z ----------------------------------------------------------------

The {mod}~cellrank.estimators allowo you to analyze cell-state dynamics. We initialize the GPCCA estimator...

However, this and other estimators with with every CellRank {mod}kernel <cellrank.kernels>.

Marius1311 commented on 2023-06-13T15:19:53Z ----------------------------------------------------------------

ok.

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michalk8 commented on 2023-06-13T01:10:33Z ----------------------------------------------------------------

as we explain -> as explained

Marius1311 commented on 2023-06-13T15:20:53Z ----------------------------------------------------------------

well...

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michalk8 commented on 2023-06-13T01:10:34Z ----------------------------------------------------------------

"We'll demonstrate both modes in this tutorial."

There's a way to add links to section headers in myst, see, e.g., here: https://myst-parser.readthedocs.io/en/latest/syntax/cross-referencing.html#implicit-targets

{meth}schur decomposition-> {meth}Schur decomposition

Marius1311 commented on 2023-06-13T15:26:19Z ----------------------------------------------------------------

ok, done.

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michalk8 commented on 2023-06-13T01:10:35Z ----------------------------------------------------------------

Add links to fit() and predict() using the {meth} role.

Marius1311 commented on 2023-06-13T15:26:52Z ----------------------------------------------------------------

I removed these from the section heading.

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michalk8 commented on 2023-06-13T01:10:36Z ----------------------------------------------------------------

Two spaces in "algorithm as"

as implemented in the pyGPCCA package (cite the zenodo)

Marius1311 commented on 2023-06-13T15:27:43Z ----------------------------------------------------------------

included already (reuter:22)

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michalk8 commented on 2023-06-13T01:10:38Z ----------------------------------------------------------------

CellRank corases-grains -> CellRank coarse-grains.

If I remember correctly, cellrank.estimators.GPCCA.macrostates is the hard assignment,cellrank.estimators.GPCCA.macrostates_memberships (please check) is the soft assignment.

Marius1311 commented on 2023-06-13T15:31:04Z ----------------------------------------------------------------

you're right, that seems to be the case. adapted.

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michalk8 commented on 2023-06-13T01:10:39Z ----------------------------------------------------------------

Can we please remove the horizontal and vertical lines + fix the figure aspect ratio?

Marius1311 commented on 2023-06-13T15:46:12Z ----------------------------------------------------------------

I don't know how

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michalk8 commented on 2023-06-13T01:10:40Z ----------------------------------------------------------------

adata.obs['clusters'] -> {attr}adata.obs['clusters'] <anndata.AnnData.obs>.

{mod}pyGPCCA doesn't link to anything

for more infos -> for more information.

Marius1311 commented on 2023-06-13T15:47:47Z ----------------------------------------------------------------

done.

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michalk8 commented on 2023-06-13T01:10:40Z ----------------------------------------------------------------

When mentioning PETSc/SLEPc, would consider adding the conda install -c conda-forge petsc4py slepc4py

Please don't hardcode the link to installation instructions, use the proper {doc}.

Marius1311 commented on 2023-06-13T15:50:48Z ----------------------------------------------------------------

ok, done

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michalk8 commented on 2023-06-13T01:10:42Z ----------------------------------------------------------------

"we use the ... method to identify the terminal states."

Marius1311 commented on 2023-06-13T15:51:24Z ----------------------------------------------------------------

ok.

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michalk8 commented on 2023-06-13T01:10:43Z ----------------------------------------------------------------

continious -> continuous

Marius1311 commented on 2023-06-13T15:52:01Z ----------------------------------------------------------------

ok, done.

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michalk8 commented on 2023-06-13T01:10:44Z ----------------------------------------------------------------

Maybe mention higher intensity/saturation means higher certainty.

Marius1311 commented on 2023-06-13T15:54:18Z ----------------------------------------------------------------

done.

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michalk8 commented on 2023-06-13T01:10:45Z ----------------------------------------------------------------

states using the {meth}... method.

Marius1311 commented on 2023-06-13T15:55:41Z ----------------------------------------------------------------

done.

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michalk8 commented on 2023-06-13T01:10:46Z ----------------------------------------------------------------

"and can be inspected conveniently."

I'd have expected you should g.initial_states and g.terminal_states

Marius1311 commented on 2023-06-13T16:01:44Z ----------------------------------------------------------------

Ok, I added that.

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michalk8 commented on 2023-06-13T01:10:47Z ----------------------------------------------------------------

inintial -> initial

Marius1311 commented on 2023-06-13T16:02:45Z ----------------------------------------------------------------

thanks.

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michalk8 commented on 2023-06-13T01:10:48Z ----------------------------------------------------------------

initial- -> initial

Marius1311 commented on 2023-06-13T16:03:01Z ----------------------------------------------------------------

done.

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michalk8 commented on 2023-06-13T01:10:49Z ----------------------------------------------------------------

Would not use italics for terminal.

knowlege -> knowledge

which we show below -> as shown below.

Marius1311 commented on 2023-06-13T16:03:44Z ----------------------------------------------------------------

ok.

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michalk8 commented on 2023-06-13T01:10:50Z ----------------------------------------------------------------

probabilits -> probability

Marius1311 commented on 2023-06-13T16:04:09Z ----------------------------------------------------------------

done.

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michalk8 commented on 2023-06-13T01:10:51Z ----------------------------------------------------------------

we compute the macrostates.

dashed vertical line

Marius1311 commented on 2023-06-13T16:04:49Z ----------------------------------------------------------------

ok.

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michalk8 commented on 2023-06-13T01:10:52Z ----------------------------------------------------------------

Remove the Nice!

...; however, that does -> . However, that does not

Missing . in the last sentence.

; we show below -> . We show below

" for each of the cells most confidently assigned to a certain macrostates" reads not so easily

Marius1311 commented on 2023-06-13T16:06:30Z ----------------------------------------------------------------

thanks, done

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michalk8 commented on 2023-06-13T01:10:53Z ----------------------------------------------------------------

any {attr}... -> any observation-level covariate

Link to the transport map kernel tutorial rather than the class (or both) (also missing the {class} role for the kernel).

Marius1311 commented on 2023-06-13T16:09:29Z ----------------------------------------------------------------

done.

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michalk8 commented on 2023-06-13T01:10:54Z ----------------------------------------------------------------

becasue -> because

Let's try the automatic terminal

Marius1311 commented on 2023-06-13T16:10:54Z ----------------------------------------------------------------

done.

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michalk8 commented on 2023-06-13T01:10:54Z ----------------------------------------------------------------

ductal-cell markers -> Ductal cell markers.

Marius1311 commented on 2023-06-13T16:11:44Z ----------------------------------------------------------------

done.

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michalk8 commented on 2023-06-13T01:10:55Z ----------------------------------------------------------------

as initial -> as an initial state.

Marius1311 commented on 2023-06-13T16:12:02Z ----------------------------------------------------------------

ok.

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michalk8 commented on 2023-06-13T01:10:56Z ----------------------------------------------------------------

we recommend... -> we recommend to: + go thrgouh/take a look/take a look/

Marius1311 commented on 2023-06-13T16:12:46Z ----------------------------------------------------------------

thanks!

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michalk8 commented on 2023-06-13T01:15:06Z ----------------------------------------------------------------

{attr) -> {attr}

Marius1311 commented on 2023-06-13T16:10:10Z ----------------------------------------------------------------

done.

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michalk8 commented on 2023-06-13T01:15:07Z ----------------------------------------------------------------

compute the {attr}fate probabilities <...> .

Marius1311 commented on 2023-06-13T16:11:19Z ----------------------------------------------------------------

done.

Marius1311 commented 1 year ago

makes sense. I moved it.

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Marius1311 commented 1 year ago

yes, I'll change this everywhere.

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Marius1311 commented 1 year ago

ok.

---

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Marius1311 commented 1 year ago

done.

---

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Marius1311 commented 1 year ago

I moved it to the first paragraph.

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Marius1311 commented 1 year ago

ok, adapted.

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Marius1311 commented 1 year ago

done, thanks!

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Marius1311 commented 1 year ago

ok.

---

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Marius1311 commented 1 year ago

well...

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Marius1311 commented 1 year ago

ok, done.

---

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Marius1311 commented 1 year ago

I removed these from the section heading.

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Marius1311 commented 1 year ago

included already (reuter:22)

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Marius1311 commented 1 year ago

you're right, that seems to be the case. adapted.

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michalk8 commented on 2023-06-13T01:10:32Z ----------------------------------------------------------------

The {mod}~cellrank.estimators allowo you to analyze cell-state dynamics. We initialize the GPCCA estimator...

However, this and other estimators with with every CellRank {mod}kernel <cellrank.kernels>.

Marius1311 commented on 2023-06-13T15:19:53Z ----------------------------------------------------------------

ok.

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michalk8 commented on 2023-06-13T01:10:33Z ----------------------------------------------------------------

as we explain -> as explained

Marius1311 commented on 2023-06-13T15:20:53Z ----------------------------------------------------------------

well...

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michalk8 commented on 2023-06-13T01:10:34Z ----------------------------------------------------------------

"We'll demonstrate both modes in this tutorial."

There's a way to add links to section headers in myst, see, e.g., here: https://myst-parser.readthedocs.io/en/latest/syntax/cross-referencing.html#implicit-targets

{meth}schur decomposition-> {meth}Schur decomposition

Marius1311 commented on 2023-06-13T15:26:19Z ----------------------------------------------------------------

ok, done.

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michalk8 commented on 2023-06-13T01:10:35Z ----------------------------------------------------------------

Add links to fit() and predict() using the {meth} role.

Marius1311 commented on 2023-06-13T15:26:52Z ----------------------------------------------------------------

I removed these from the section heading.

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michalk8 commented on 2023-06-13T01:10:36Z ----------------------------------------------------------------

Two spaces in "algorithm as"

as implemented in the pyGPCCA package (cite the zenodo)

Marius1311 commented on 2023-06-13T15:27:43Z ----------------------------------------------------------------

included already (reuter:22)

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michalk8 commented on 2023-06-13T01:10:38Z ----------------------------------------------------------------

CellRank corases-grains -> CellRank coarse-grains.

If I remember correctly, cellrank.estimators.GPCCA.macrostates is the hard assignment,cellrank.estimators.GPCCA.macrostates_memberships (please check) is the soft assignment.

Marius1311 commented on 2023-06-13T15:31:04Z ----------------------------------------------------------------

you're right, that seems to be the case. adapted.

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michalk8 commented on 2023-06-13T01:10:39Z ----------------------------------------------------------------

Can we please remove the horizontal and vertical lines + fix the figure aspect ratio?

Marius1311 commented on 2023-06-13T15:46:12Z ----------------------------------------------------------------

I don't know how

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michalk8 commented on 2023-06-13T01:10:40Z ----------------------------------------------------------------

adata.obs['clusters'] -> {attr}adata.obs['clusters'] <anndata.AnnData.obs>.

{mod}pyGPCCA doesn't link to anything

for more infos -> for more information.

Marius1311 commented on 2023-06-13T15:47:47Z ----------------------------------------------------------------

done.

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michalk8 commented on 2023-06-13T01:10:40Z ----------------------------------------------------------------

When mentioning PETSc/SLEPc, would consider adding the conda install -c conda-forge petsc4py slepc4py

Please don't hardcode the link to installation instructions, use the proper {doc}.

Marius1311 commented on 2023-06-13T15:50:48Z ----------------------------------------------------------------

ok, done

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michalk8 commented on 2023-06-13T01:10:42Z ----------------------------------------------------------------

"we use the ... method to identify the terminal states."

Marius1311 commented on 2023-06-13T15:51:24Z ----------------------------------------------------------------

ok.

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michalk8 commented on 2023-06-13T01:10:43Z ----------------------------------------------------------------

continious -> continuous

Marius1311 commented on 2023-06-13T15:52:01Z ----------------------------------------------------------------

ok, done.

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michalk8 commented on 2023-06-13T01:10:44Z ----------------------------------------------------------------

Maybe mention higher intensity/saturation means higher certainty.

Marius1311 commented on 2023-06-13T15:54:18Z ----------------------------------------------------------------

done.

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michalk8 commented on 2023-06-13T01:10:45Z ----------------------------------------------------------------

states using the {meth}... method.

Marius1311 commented on 2023-06-13T15:55:41Z ----------------------------------------------------------------

done.

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michalk8 commented on 2023-06-13T01:10:46Z ----------------------------------------------------------------

"and can be inspected conveniently."

I'd have expected you should g.initial_states and g.terminal_states

Marius1311 commented on 2023-06-13T16:01:44Z ----------------------------------------------------------------

Ok, I added that.

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michalk8 commented on 2023-06-13T01:10:47Z ----------------------------------------------------------------

inintial -> initial

Marius1311 commented on 2023-06-13T16:02:45Z ----------------------------------------------------------------

thanks.

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michalk8 commented on 2023-06-13T01:10:48Z ----------------------------------------------------------------

initial- -> initial

Marius1311 commented on 2023-06-13T16:03:01Z ----------------------------------------------------------------

done.

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michalk8 commented on 2023-06-13T01:10:49Z ----------------------------------------------------------------

Would not use italics for terminal.

knowlege -> knowledge

which we show below -> as shown below.

Marius1311 commented on 2023-06-13T16:03:44Z ----------------------------------------------------------------

ok.

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michalk8 commented on 2023-06-13T01:10:50Z ----------------------------------------------------------------

probabilits -> probability

Marius1311 commented on 2023-06-13T16:04:09Z ----------------------------------------------------------------

done.

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michalk8 commented on 2023-06-13T01:10:51Z ----------------------------------------------------------------

we compute the macrostates.

dashed vertical line

Marius1311 commented on 2023-06-13T16:04:49Z ----------------------------------------------------------------

ok.

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michalk8 commented on 2023-06-13T01:10:52Z ----------------------------------------------------------------

Remove the Nice!

...; however, that does -> . However, that does not

Missing . in the last sentence.

; we show below -> . We show below

" for each of the cells most confidently assigned to a certain macrostates" reads not so easily

Marius1311 commented on 2023-06-13T16:06:30Z ----------------------------------------------------------------

thanks, done

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michalk8 commented on 2023-06-13T01:10:53Z ----------------------------------------------------------------

any {attr}... -> any observation-level covariate

Link to the transport map kernel tutorial rather than the class (or both) (also missing the {class} role for the kernel).

Marius1311 commented on 2023-06-13T16:09:29Z ----------------------------------------------------------------

done.

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michalk8 commented on 2023-06-13T01:10:54Z ----------------------------------------------------------------

becasue -> because

Let's try the automatic terminal

Marius1311 commented on 2023-06-13T16:10:54Z ----------------------------------------------------------------

done.

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michalk8 commented on 2023-06-13T01:10:54Z ----------------------------------------------------------------

ductal-cell markers -> Ductal cell markers.

Marius1311 commented on 2023-06-13T16:11:44Z ----------------------------------------------------------------

done.

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michalk8 commented on 2023-06-13T01:10:55Z ----------------------------------------------------------------

as initial -> as an initial state.

Marius1311 commented on 2023-06-13T16:12:02Z ----------------------------------------------------------------

ok.

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michalk8 commented on 2023-06-13T01:10:56Z ----------------------------------------------------------------

we recommend... -> we recommend to: + go thrgouh/take a look/take a look/

Marius1311 commented on 2023-06-13T16:12:46Z ----------------------------------------------------------------

thanks!

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michalk8 commented on 2023-06-13T01:15:06Z ----------------------------------------------------------------

{attr) -> {attr}

Marius1311 commented on 2023-06-13T16:10:10Z ----------------------------------------------------------------

done.

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michalk8 commented on 2023-06-13T01:15:07Z ----------------------------------------------------------------

compute the {attr}fate probabilities <...> .

Marius1311 commented on 2023-06-13T16:11:19Z ----------------------------------------------------------------

done.

Marius1311 commented 1 year ago

makes sense. I moved it.

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Marius1311 commented 1 year ago

yes, I'll change this everywhere.

---

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Marius1311 commented 1 year ago

ok.

---

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Marius1311 commented 1 year ago

done.

---

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Marius1311 commented 1 year ago

I moved it to the first paragraph.

---

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Marius1311 commented 1 year ago

ok, adapted.

---

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Marius1311 commented 1 year ago

done, thanks!

---

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Marius1311 commented 1 year ago

ok.

---

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Marius1311 commented 1 year ago

well...

---

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Marius1311 commented 1 year ago

ok, done.

---

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Marius1311 commented 1 year ago

I removed these from the section heading.

---

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Marius1311 commented 1 year ago

included already (reuter:22)

---

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Marius1311 commented 1 year ago

you're right, that seems to be the case. adapted.

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michalk8 commented on 2023-06-13T01:10:33Z ----------------------------------------------------------------

as we explain -> as explained

Marius1311 commented on 2023-06-13T15:20:53Z ----------------------------------------------------------------

well...

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michalk8 commented on 2023-06-13T01:10:34Z ----------------------------------------------------------------

"We'll demonstrate both modes in this tutorial."

There's a way to add links to section headers in myst, see, e.g., here: https://myst-parser.readthedocs.io/en/latest/syntax/cross-referencing.html#implicit-targets

{meth}schur decomposition-> {meth}Schur decomposition

Marius1311 commented on 2023-06-13T15:26:19Z ----------------------------------------------------------------

ok, done.

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michalk8 commented on 2023-06-13T01:10:35Z ----------------------------------------------------------------

Add links to fit() and predict() using the {meth} role.

Marius1311 commented on 2023-06-13T15:26:52Z ----------------------------------------------------------------

I removed these from the section heading.

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michalk8 commented on 2023-06-13T01:10:36Z ----------------------------------------------------------------

Two spaces in "algorithm as"

as implemented in the pyGPCCA package (cite the zenodo)

Marius1311 commented on 2023-06-13T15:27:43Z ----------------------------------------------------------------

included already (reuter:22)

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michalk8 commented on 2023-06-13T01:10:38Z ----------------------------------------------------------------

CellRank corases-grains -> CellRank coarse-grains.

If I remember correctly, cellrank.estimators.GPCCA.macrostates is the hard assignment,cellrank.estimators.GPCCA.macrostates_memberships (please check) is the soft assignment.

Marius1311 commented on 2023-06-13T15:31:04Z ----------------------------------------------------------------

you're right, that seems to be the case. adapted.

review-notebook-app[bot] commented 1 year ago

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michalk8 commented on 2023-06-13T01:10:39Z ----------------------------------------------------------------

Can we please remove the horizontal and vertical lines + fix the figure aspect ratio?

Marius1311 commented on 2023-06-13T15:46:12Z ----------------------------------------------------------------

I don't know how

review-notebook-app[bot] commented 1 year ago

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michalk8 commented on 2023-06-13T01:10:40Z ----------------------------------------------------------------

adata.obs['clusters'] -> {attr}adata.obs['clusters'] <anndata.AnnData.obs>.

{mod}pyGPCCA doesn't link to anything

for more infos -> for more information.

Marius1311 commented on 2023-06-13T15:47:47Z ----------------------------------------------------------------

done.

review-notebook-app[bot] commented 1 year ago

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michalk8 commented on 2023-06-13T01:10:40Z ----------------------------------------------------------------

When mentioning PETSc/SLEPc, would consider adding the conda install -c conda-forge petsc4py slepc4py

Please don't hardcode the link to installation instructions, use the proper {doc}.

Marius1311 commented on 2023-06-13T15:50:48Z ----------------------------------------------------------------

ok, done

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michalk8 commented on 2023-06-13T01:10:42Z ----------------------------------------------------------------

"we use the ... method to identify the terminal states."

Marius1311 commented on 2023-06-13T15:51:24Z ----------------------------------------------------------------

ok.

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michalk8 commented on 2023-06-13T01:10:43Z ----------------------------------------------------------------

continious -> continuous

Marius1311 commented on 2023-06-13T15:52:01Z ----------------------------------------------------------------

ok, done.

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michalk8 commented on 2023-06-13T01:10:44Z ----------------------------------------------------------------

Maybe mention higher intensity/saturation means higher certainty.

Marius1311 commented on 2023-06-13T15:54:18Z ----------------------------------------------------------------

done.

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michalk8 commented on 2023-06-13T01:10:45Z ----------------------------------------------------------------

states using the {meth}... method.

Marius1311 commented on 2023-06-13T15:55:41Z ----------------------------------------------------------------

done.

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michalk8 commented on 2023-06-13T01:10:46Z ----------------------------------------------------------------

"and can be inspected conveniently."

I'd have expected you should g.initial_states and g.terminal_states

Marius1311 commented on 2023-06-13T16:01:44Z ----------------------------------------------------------------

Ok, I added that.

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michalk8 commented on 2023-06-13T01:10:47Z ----------------------------------------------------------------

inintial -> initial

Marius1311 commented on 2023-06-13T16:02:45Z ----------------------------------------------------------------

thanks.

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michalk8 commented on 2023-06-13T01:10:48Z ----------------------------------------------------------------

initial- -> initial

Marius1311 commented on 2023-06-13T16:03:01Z ----------------------------------------------------------------

done.

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michalk8 commented on 2023-06-13T01:10:49Z ----------------------------------------------------------------

Would not use italics for terminal.

knowlege -> knowledge

which we show below -> as shown below.

Marius1311 commented on 2023-06-13T16:03:44Z ----------------------------------------------------------------

ok.

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michalk8 commented on 2023-06-13T01:10:50Z ----------------------------------------------------------------

probabilits -> probability

Marius1311 commented on 2023-06-13T16:04:09Z ----------------------------------------------------------------

done.

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michalk8 commented on 2023-06-13T01:10:51Z ----------------------------------------------------------------

we compute the macrostates.

dashed vertical line

Marius1311 commented on 2023-06-13T16:04:49Z ----------------------------------------------------------------

ok.

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michalk8 commented on 2023-06-13T01:10:52Z ----------------------------------------------------------------

Remove the Nice!

...; however, that does -> . However, that does not

Missing . in the last sentence.

; we show below -> . We show below

" for each of the cells most confidently assigned to a certain macrostates" reads not so easily

Marius1311 commented on 2023-06-13T16:06:30Z ----------------------------------------------------------------

thanks, done

review-notebook-app[bot] commented 1 year ago

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michalk8 commented on 2023-06-13T01:10:53Z ----------------------------------------------------------------

any {attr}... -> any observation-level covariate

Link to the transport map kernel tutorial rather than the class (or both) (also missing the {class} role for the kernel).

Marius1311 commented on 2023-06-13T16:09:29Z ----------------------------------------------------------------

done.

review-notebook-app[bot] commented 1 year ago

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michalk8 commented on 2023-06-13T01:10:54Z ----------------------------------------------------------------

becasue -> because

Let's try the automatic terminal

Marius1311 commented on 2023-06-13T16:10:54Z ----------------------------------------------------------------

done.

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michalk8 commented on 2023-06-13T01:10:54Z ----------------------------------------------------------------

ductal-cell markers -> Ductal cell markers.

Marius1311 commented on 2023-06-13T16:11:44Z ----------------------------------------------------------------

done.

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michalk8 commented on 2023-06-13T01:10:55Z ----------------------------------------------------------------

as initial -> as an initial state.

Marius1311 commented on 2023-06-13T16:12:02Z ----------------------------------------------------------------

ok.

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michalk8 commented on 2023-06-13T01:10:56Z ----------------------------------------------------------------

we recommend... -> we recommend to: + go thrgouh/take a look/take a look/

Marius1311 commented on 2023-06-13T16:12:46Z ----------------------------------------------------------------

thanks!

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michalk8 commented on 2023-06-13T01:15:06Z ----------------------------------------------------------------

{attr) -> {attr}

Marius1311 commented on 2023-06-13T16:10:10Z ----------------------------------------------------------------

done.

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michalk8 commented on 2023-06-13T01:15:07Z ----------------------------------------------------------------

compute the {attr}fate probabilities <...> .

Marius1311 commented on 2023-06-13T16:11:19Z ----------------------------------------------------------------

done.

Marius1311 commented 1 year ago

makes sense. I moved it.

---

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Marius1311 commented 1 year ago

yes, I'll change this everywhere.

---

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Marius1311 commented 1 year ago

ok.

---

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Marius1311 commented 1 year ago

done.

---

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Marius1311 commented 1 year ago

I moved it to the first paragraph.

---

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Marius1311 commented 1 year ago

ok, adapted.

---

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Marius1311 commented 1 year ago

done, thanks!

---

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Marius1311 commented 1 year ago

ok.

---

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Marius1311 commented 1 year ago

well...

---

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Marius1311 commented 1 year ago

ok, done.

---

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Marius1311 commented 1 year ago

I removed these from the section heading.

---

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Marius1311 commented 1 year ago

included already (reuter:22)

---

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Marius1311 commented 1 year ago

you're right, that seems to be the case. adapted.

---

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michalk8 commented on 2023-06-13T01:10:34Z ----------------------------------------------------------------

"We'll demonstrate both modes in this tutorial."

There's a way to add links to section headers in myst, see, e.g., here: https://myst-parser.readthedocs.io/en/latest/syntax/cross-referencing.html#implicit-targets

{meth}schur decomposition-> {meth}Schur decomposition

Marius1311 commented on 2023-06-13T15:26:19Z ----------------------------------------------------------------

ok, done.

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michalk8 commented on 2023-06-13T01:10:35Z ----------------------------------------------------------------

Add links to fit() and predict() using the {meth} role.

Marius1311 commented on 2023-06-13T15:26:52Z ----------------------------------------------------------------

I removed these from the section heading.

review-notebook-app[bot] commented 1 year ago

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michalk8 commented on 2023-06-13T01:10:36Z ----------------------------------------------------------------

Two spaces in "algorithm as"

as implemented in the pyGPCCA package (cite the zenodo)

Marius1311 commented on 2023-06-13T15:27:43Z ----------------------------------------------------------------

included already (reuter:22)

review-notebook-app[bot] commented 1 year ago

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michalk8 commented on 2023-06-13T01:10:38Z ----------------------------------------------------------------

CellRank corases-grains -> CellRank coarse-grains.

If I remember correctly, cellrank.estimators.GPCCA.macrostates is the hard assignment,cellrank.estimators.GPCCA.macrostates_memberships (please check) is the soft assignment.

Marius1311 commented on 2023-06-13T15:31:04Z ----------------------------------------------------------------

you're right, that seems to be the case. adapted.

review-notebook-app[bot] commented 1 year ago

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michalk8 commented on 2023-06-13T01:10:39Z ----------------------------------------------------------------

Can we please remove the horizontal and vertical lines + fix the figure aspect ratio?

Marius1311 commented on 2023-06-13T15:46:12Z ----------------------------------------------------------------

I don't know how

review-notebook-app[bot] commented 1 year ago

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michalk8 commented on 2023-06-13T01:10:40Z ----------------------------------------------------------------

adata.obs['clusters'] -> {attr}adata.obs['clusters'] <anndata.AnnData.obs>.

{mod}pyGPCCA doesn't link to anything

for more infos -> for more information.

Marius1311 commented on 2023-06-13T15:47:47Z ----------------------------------------------------------------

done.

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michalk8 commented on 2023-06-13T01:10:40Z ----------------------------------------------------------------

When mentioning PETSc/SLEPc, would consider adding the conda install -c conda-forge petsc4py slepc4py

Please don't hardcode the link to installation instructions, use the proper {doc}.

Marius1311 commented on 2023-06-13T15:50:48Z ----------------------------------------------------------------

ok, done

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michalk8 commented on 2023-06-13T01:10:42Z ----------------------------------------------------------------

"we use the ... method to identify the terminal states."

Marius1311 commented on 2023-06-13T15:51:24Z ----------------------------------------------------------------

ok.

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michalk8 commented on 2023-06-13T01:10:43Z ----------------------------------------------------------------

continious -> continuous

Marius1311 commented on 2023-06-13T15:52:01Z ----------------------------------------------------------------

ok, done.

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michalk8 commented on 2023-06-13T01:10:44Z ----------------------------------------------------------------

Maybe mention higher intensity/saturation means higher certainty.

Marius1311 commented on 2023-06-13T15:54:18Z ----------------------------------------------------------------

done.

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michalk8 commented on 2023-06-13T01:10:45Z ----------------------------------------------------------------

states using the {meth}... method.

Marius1311 commented on 2023-06-13T15:55:41Z ----------------------------------------------------------------

done.

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michalk8 commented on 2023-06-13T01:10:46Z ----------------------------------------------------------------

"and can be inspected conveniently."

I'd have expected you should g.initial_states and g.terminal_states

Marius1311 commented on 2023-06-13T16:01:44Z ----------------------------------------------------------------

Ok, I added that.

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michalk8 commented on 2023-06-13T01:10:47Z ----------------------------------------------------------------

inintial -> initial

Marius1311 commented on 2023-06-13T16:02:45Z ----------------------------------------------------------------

thanks.

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michalk8 commented on 2023-06-13T01:10:48Z ----------------------------------------------------------------

initial- -> initial

Marius1311 commented on 2023-06-13T16:03:01Z ----------------------------------------------------------------

done.

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michalk8 commented on 2023-06-13T01:10:49Z ----------------------------------------------------------------

Would not use italics for terminal.

knowlege -> knowledge

which we show below -> as shown below.

Marius1311 commented on 2023-06-13T16:03:44Z ----------------------------------------------------------------

ok.

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michalk8 commented on 2023-06-13T01:10:50Z ----------------------------------------------------------------

probabilits -> probability

Marius1311 commented on 2023-06-13T16:04:09Z ----------------------------------------------------------------

done.

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michalk8 commented on 2023-06-13T01:10:51Z ----------------------------------------------------------------

we compute the macrostates.

dashed vertical line

Marius1311 commented on 2023-06-13T16:04:49Z ----------------------------------------------------------------

ok.

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michalk8 commented on 2023-06-13T01:10:52Z ----------------------------------------------------------------

Remove the Nice!

...; however, that does -> . However, that does not

Missing . in the last sentence.

; we show below -> . We show below

" for each of the cells most confidently assigned to a certain macrostates" reads not so easily

Marius1311 commented on 2023-06-13T16:06:30Z ----------------------------------------------------------------

thanks, done

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michalk8 commented on 2023-06-13T01:10:53Z ----------------------------------------------------------------

any {attr}... -> any observation-level covariate

Link to the transport map kernel tutorial rather than the class (or both) (also missing the {class} role for the kernel).

Marius1311 commented on 2023-06-13T16:09:29Z ----------------------------------------------------------------

done.

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michalk8 commented on 2023-06-13T01:10:54Z ----------------------------------------------------------------

becasue -> because

Let's try the automatic terminal

Marius1311 commented on 2023-06-13T16:10:54Z ----------------------------------------------------------------

done.

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michalk8 commented on 2023-06-13T01:10:54Z ----------------------------------------------------------------

ductal-cell markers -> Ductal cell markers.

Marius1311 commented on 2023-06-13T16:11:44Z ----------------------------------------------------------------

done.

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michalk8 commented on 2023-06-13T01:10:55Z ----------------------------------------------------------------

as initial -> as an initial state.

Marius1311 commented on 2023-06-13T16:12:02Z ----------------------------------------------------------------

ok.

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michalk8 commented on 2023-06-13T01:10:56Z ----------------------------------------------------------------

we recommend... -> we recommend to: + go thrgouh/take a look/take a look/

Marius1311 commented on 2023-06-13T16:12:46Z ----------------------------------------------------------------

thanks!

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michalk8 commented on 2023-06-13T01:15:06Z ----------------------------------------------------------------

{attr) -> {attr}

Marius1311 commented on 2023-06-13T16:10:10Z ----------------------------------------------------------------

done.

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michalk8 commented on 2023-06-13T01:15:07Z ----------------------------------------------------------------

compute the {attr}fate probabilities <...> .

Marius1311 commented on 2023-06-13T16:11:19Z ----------------------------------------------------------------

done.

Marius1311 commented 1 year ago

makes sense. I moved it.

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Marius1311 commented 1 year ago

yes, I'll change this everywhere.

---

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Marius1311 commented 1 year ago

ok.

---

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Marius1311 commented 1 year ago

done.

---

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Marius1311 commented 1 year ago

I moved it to the first paragraph.

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Marius1311 commented 1 year ago

ok, adapted.

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Marius1311 commented 1 year ago

done, thanks!

---

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Marius1311 commented 1 year ago

ok.

---

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Marius1311 commented 1 year ago

well...

---

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Marius1311 commented 1 year ago

ok, done.

---

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Marius1311 commented 1 year ago

I removed these from the section heading.

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Marius1311 commented 1 year ago

included already (reuter:22)

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Marius1311 commented 1 year ago

you're right, that seems to be the case. adapted.

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michalk8 commented on 2023-06-13T01:10:35Z ----------------------------------------------------------------

Add links to fit() and predict() using the {meth} role.

Marius1311 commented on 2023-06-13T15:26:52Z ----------------------------------------------------------------

I removed these from the section heading.

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michalk8 commented on 2023-06-13T01:10:36Z ----------------------------------------------------------------

Two spaces in "algorithm as"

as implemented in the pyGPCCA package (cite the zenodo)

Marius1311 commented on 2023-06-13T15:27:43Z ----------------------------------------------------------------

included already (reuter:22)

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michalk8 commented on 2023-06-13T01:10:38Z ----------------------------------------------------------------

CellRank corases-grains -> CellRank coarse-grains.

If I remember correctly, cellrank.estimators.GPCCA.macrostates is the hard assignment,cellrank.estimators.GPCCA.macrostates_memberships (please check) is the soft assignment.

Marius1311 commented on 2023-06-13T15:31:04Z ----------------------------------------------------------------

you're right, that seems to be the case. adapted.

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michalk8 commented on 2023-06-13T01:10:39Z ----------------------------------------------------------------

Can we please remove the horizontal and vertical lines + fix the figure aspect ratio?

Marius1311 commented on 2023-06-13T15:46:12Z ----------------------------------------------------------------

I don't know how

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michalk8 commented on 2023-06-13T01:10:40Z ----------------------------------------------------------------

adata.obs['clusters'] -> {attr}adata.obs['clusters'] <anndata.AnnData.obs>.

{mod}pyGPCCA doesn't link to anything

for more infos -> for more information.

Marius1311 commented on 2023-06-13T15:47:47Z ----------------------------------------------------------------

done.

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michalk8 commented on 2023-06-13T01:10:40Z ----------------------------------------------------------------

When mentioning PETSc/SLEPc, would consider adding the conda install -c conda-forge petsc4py slepc4py

Please don't hardcode the link to installation instructions, use the proper {doc}.

Marius1311 commented on 2023-06-13T15:50:48Z ----------------------------------------------------------------

ok, done

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michalk8 commented on 2023-06-13T01:10:42Z ----------------------------------------------------------------

"we use the ... method to identify the terminal states."

Marius1311 commented on 2023-06-13T15:51:24Z ----------------------------------------------------------------

ok.

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michalk8 commented on 2023-06-13T01:10:43Z ----------------------------------------------------------------

continious -> continuous

Marius1311 commented on 2023-06-13T15:52:01Z ----------------------------------------------------------------

ok, done.

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michalk8 commented on 2023-06-13T01:10:44Z ----------------------------------------------------------------

Maybe mention higher intensity/saturation means higher certainty.

Marius1311 commented on 2023-06-13T15:54:18Z ----------------------------------------------------------------

done.

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michalk8 commented on 2023-06-13T01:10:45Z ----------------------------------------------------------------

states using the {meth}... method.

Marius1311 commented on 2023-06-13T15:55:41Z ----------------------------------------------------------------

done.

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michalk8 commented on 2023-06-13T01:10:46Z ----------------------------------------------------------------

"and can be inspected conveniently."

I'd have expected you should g.initial_states and g.terminal_states

Marius1311 commented on 2023-06-13T16:01:44Z ----------------------------------------------------------------

Ok, I added that.

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michalk8 commented on 2023-06-13T01:10:47Z ----------------------------------------------------------------

inintial -> initial

Marius1311 commented on 2023-06-13T16:02:45Z ----------------------------------------------------------------

thanks.

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michalk8 commented on 2023-06-13T01:10:48Z ----------------------------------------------------------------

initial- -> initial

Marius1311 commented on 2023-06-13T16:03:01Z ----------------------------------------------------------------

done.

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michalk8 commented on 2023-06-13T01:10:49Z ----------------------------------------------------------------

Would not use italics for terminal.

knowlege -> knowledge

which we show below -> as shown below.

Marius1311 commented on 2023-06-13T16:03:44Z ----------------------------------------------------------------

ok.

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michalk8 commented on 2023-06-13T01:10:50Z ----------------------------------------------------------------

probabilits -> probability

Marius1311 commented on 2023-06-13T16:04:09Z ----------------------------------------------------------------

done.

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michalk8 commented on 2023-06-13T01:10:51Z ----------------------------------------------------------------

we compute the macrostates.

dashed vertical line

Marius1311 commented on 2023-06-13T16:04:49Z ----------------------------------------------------------------

ok.

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michalk8 commented on 2023-06-13T01:10:52Z ----------------------------------------------------------------

Remove the Nice!

...; however, that does -> . However, that does not

Missing . in the last sentence.

; we show below -> . We show below

" for each of the cells most confidently assigned to a certain macrostates" reads not so easily

Marius1311 commented on 2023-06-13T16:06:30Z ----------------------------------------------------------------

thanks, done

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michalk8 commented on 2023-06-13T01:10:53Z ----------------------------------------------------------------

any {attr}... -> any observation-level covariate

Link to the transport map kernel tutorial rather than the class (or both) (also missing the {class} role for the kernel).

Marius1311 commented on 2023-06-13T16:09:29Z ----------------------------------------------------------------

done.

review-notebook-app[bot] commented 1 year ago

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michalk8 commented on 2023-06-13T01:10:54Z ----------------------------------------------------------------

becasue -> because

Let's try the automatic terminal

Marius1311 commented on 2023-06-13T16:10:54Z ----------------------------------------------------------------

done.

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michalk8 commented on 2023-06-13T01:10:54Z ----------------------------------------------------------------

ductal-cell markers -> Ductal cell markers.

Marius1311 commented on 2023-06-13T16:11:44Z ----------------------------------------------------------------

done.

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michalk8 commented on 2023-06-13T01:10:55Z ----------------------------------------------------------------

as initial -> as an initial state.

Marius1311 commented on 2023-06-13T16:12:02Z ----------------------------------------------------------------

ok.

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michalk8 commented on 2023-06-13T01:10:56Z ----------------------------------------------------------------

we recommend... -> we recommend to: + go thrgouh/take a look/take a look/

Marius1311 commented on 2023-06-13T16:12:46Z ----------------------------------------------------------------

thanks!

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michalk8 commented on 2023-06-13T01:15:06Z ----------------------------------------------------------------

{attr) -> {attr}

Marius1311 commented on 2023-06-13T16:10:10Z ----------------------------------------------------------------

done.

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michalk8 commented on 2023-06-13T01:15:07Z ----------------------------------------------------------------

compute the {attr}fate probabilities <...> .

Marius1311 commented on 2023-06-13T16:11:19Z ----------------------------------------------------------------

done.

Marius1311 commented 1 year ago

makes sense. I moved it.

---

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Marius1311 commented 1 year ago

yes, I'll change this everywhere.

---

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Marius1311 commented 1 year ago

ok.

---

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Marius1311 commented 1 year ago

done.

---

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Marius1311 commented 1 year ago

I moved it to the first paragraph.

---

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Marius1311 commented 1 year ago

ok, adapted.

---

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Marius1311 commented 1 year ago

done, thanks!

---

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Marius1311 commented 1 year ago

ok.

---

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Marius1311 commented 1 year ago

well...

---

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Marius1311 commented 1 year ago

ok, done.

---

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Marius1311 commented 1 year ago

I removed these from the section heading.

---

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Marius1311 commented 1 year ago

included already (reuter:22)

---

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Marius1311 commented 1 year ago

you're right, that seems to be the case. adapted.

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michalk8 commented on 2023-06-13T01:10:36Z ----------------------------------------------------------------

Two spaces in "algorithm as"

as implemented in the pyGPCCA package (cite the zenodo)

Marius1311 commented on 2023-06-13T15:27:43Z ----------------------------------------------------------------

included already (reuter:22)

review-notebook-app[bot] commented 1 year ago

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michalk8 commented on 2023-06-13T01:10:38Z ----------------------------------------------------------------

CellRank corases-grains -> CellRank coarse-grains.

If I remember correctly, cellrank.estimators.GPCCA.macrostates is the hard assignment,cellrank.estimators.GPCCA.macrostates_memberships (please check) is the soft assignment.

Marius1311 commented on 2023-06-13T15:31:04Z ----------------------------------------------------------------

you're right, that seems to be the case. adapted.

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michalk8 commented on 2023-06-13T01:10:39Z ----------------------------------------------------------------

Can we please remove the horizontal and vertical lines + fix the figure aspect ratio?

Marius1311 commented on 2023-06-13T15:46:12Z ----------------------------------------------------------------

I don't know how

review-notebook-app[bot] commented 1 year ago

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michalk8 commented on 2023-06-13T01:10:40Z ----------------------------------------------------------------

adata.obs['clusters'] -> {attr}adata.obs['clusters'] <anndata.AnnData.obs>.

{mod}pyGPCCA doesn't link to anything

for more infos -> for more information.

Marius1311 commented on 2023-06-13T15:47:47Z ----------------------------------------------------------------

done.

review-notebook-app[bot] commented 1 year ago

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michalk8 commented on 2023-06-13T01:10:40Z ----------------------------------------------------------------

When mentioning PETSc/SLEPc, would consider adding the conda install -c conda-forge petsc4py slepc4py

Please don't hardcode the link to installation instructions, use the proper {doc}.

Marius1311 commented on 2023-06-13T15:50:48Z ----------------------------------------------------------------

ok, done

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michalk8 commented on 2023-06-13T01:10:42Z ----------------------------------------------------------------

"we use the ... method to identify the terminal states."

Marius1311 commented on 2023-06-13T15:51:24Z ----------------------------------------------------------------

ok.

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michalk8 commented on 2023-06-13T01:10:43Z ----------------------------------------------------------------

continious -> continuous

Marius1311 commented on 2023-06-13T15:52:01Z ----------------------------------------------------------------

ok, done.

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michalk8 commented on 2023-06-13T01:10:44Z ----------------------------------------------------------------

Maybe mention higher intensity/saturation means higher certainty.

Marius1311 commented on 2023-06-13T15:54:18Z ----------------------------------------------------------------

done.

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michalk8 commented on 2023-06-13T01:10:45Z ----------------------------------------------------------------

states using the {meth}... method.

Marius1311 commented on 2023-06-13T15:55:41Z ----------------------------------------------------------------

done.

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michalk8 commented on 2023-06-13T01:10:46Z ----------------------------------------------------------------

"and can be inspected conveniently."

I'd have expected you should g.initial_states and g.terminal_states

Marius1311 commented on 2023-06-13T16:01:44Z ----------------------------------------------------------------

Ok, I added that.

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michalk8 commented on 2023-06-13T01:10:47Z ----------------------------------------------------------------

inintial -> initial

Marius1311 commented on 2023-06-13T16:02:45Z ----------------------------------------------------------------

thanks.

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michalk8 commented on 2023-06-13T01:10:48Z ----------------------------------------------------------------

initial- -> initial

Marius1311 commented on 2023-06-13T16:03:01Z ----------------------------------------------------------------

done.

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michalk8 commented on 2023-06-13T01:10:49Z ----------------------------------------------------------------

Would not use italics for terminal.

knowlege -> knowledge

which we show below -> as shown below.

Marius1311 commented on 2023-06-13T16:03:44Z ----------------------------------------------------------------

ok.

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michalk8 commented on 2023-06-13T01:10:50Z ----------------------------------------------------------------

probabilits -> probability

Marius1311 commented on 2023-06-13T16:04:09Z ----------------------------------------------------------------

done.

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michalk8 commented on 2023-06-13T01:10:51Z ----------------------------------------------------------------

we compute the macrostates.

dashed vertical line

Marius1311 commented on 2023-06-13T16:04:49Z ----------------------------------------------------------------

ok.

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michalk8 commented on 2023-06-13T01:10:52Z ----------------------------------------------------------------

Remove the Nice!

...; however, that does -> . However, that does not

Missing . in the last sentence.

; we show below -> . We show below

" for each of the cells most confidently assigned to a certain macrostates" reads not so easily

Marius1311 commented on 2023-06-13T16:06:30Z ----------------------------------------------------------------

thanks, done

review-notebook-app[bot] commented 1 year ago

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michalk8 commented on 2023-06-13T01:10:53Z ----------------------------------------------------------------

any {attr}... -> any observation-level covariate

Link to the transport map kernel tutorial rather than the class (or both) (also missing the {class} role for the kernel).

Marius1311 commented on 2023-06-13T16:09:29Z ----------------------------------------------------------------

done.

review-notebook-app[bot] commented 1 year ago

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michalk8 commented on 2023-06-13T01:10:54Z ----------------------------------------------------------------

becasue -> because

Let's try the automatic terminal

Marius1311 commented on 2023-06-13T16:10:54Z ----------------------------------------------------------------

done.

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michalk8 commented on 2023-06-13T01:10:54Z ----------------------------------------------------------------

ductal-cell markers -> Ductal cell markers.

Marius1311 commented on 2023-06-13T16:11:44Z ----------------------------------------------------------------

done.

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michalk8 commented on 2023-06-13T01:10:55Z ----------------------------------------------------------------

as initial -> as an initial state.

Marius1311 commented on 2023-06-13T16:12:02Z ----------------------------------------------------------------

ok.

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michalk8 commented on 2023-06-13T01:10:56Z ----------------------------------------------------------------

we recommend... -> we recommend to: + go thrgouh/take a look/take a look/

Marius1311 commented on 2023-06-13T16:12:46Z ----------------------------------------------------------------

thanks!

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michalk8 commented on 2023-06-13T01:15:06Z ----------------------------------------------------------------

{attr) -> {attr}

Marius1311 commented on 2023-06-13T16:10:10Z ----------------------------------------------------------------

done.

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michalk8 commented on 2023-06-13T01:15:07Z ----------------------------------------------------------------

compute the {attr}fate probabilities <...> .

Marius1311 commented on 2023-06-13T16:11:19Z ----------------------------------------------------------------

done.

Marius1311 commented 1 year ago

makes sense. I moved it.

---

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Marius1311 commented 1 year ago

yes, I'll change this everywhere.

---

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Marius1311 commented 1 year ago

ok.

---

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Marius1311 commented 1 year ago

done.

---

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Marius1311 commented 1 year ago

I moved it to the first paragraph.

---

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Marius1311 commented 1 year ago

ok, adapted.

---

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Marius1311 commented 1 year ago

done, thanks!

---

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Marius1311 commented 1 year ago

ok.

---

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Marius1311 commented 1 year ago

well...

---

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Marius1311 commented 1 year ago

ok, done.

---

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Marius1311 commented 1 year ago

I removed these from the section heading.

---

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Marius1311 commented 1 year ago

included already (reuter:22)

---

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Marius1311 commented 1 year ago

you're right, that seems to be the case. adapted.

---

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michalk8 commented on 2023-06-13T01:10:38Z ----------------------------------------------------------------

CellRank corases-grains -> CellRank coarse-grains.

If I remember correctly, cellrank.estimators.GPCCA.macrostates is the hard assignment,cellrank.estimators.GPCCA.macrostates_memberships (please check) is the soft assignment.

Marius1311 commented on 2023-06-13T15:31:04Z ----------------------------------------------------------------

you're right, that seems to be the case. adapted.

review-notebook-app[bot] commented 1 year ago

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michalk8 commented on 2023-06-13T01:10:39Z ----------------------------------------------------------------

Can we please remove the horizontal and vertical lines + fix the figure aspect ratio?

Marius1311 commented on 2023-06-13T15:46:12Z ----------------------------------------------------------------

I don't know how

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michalk8 commented on 2023-06-13T01:10:40Z ----------------------------------------------------------------

adata.obs['clusters'] -> {attr}adata.obs['clusters'] <anndata.AnnData.obs>.

{mod}pyGPCCA doesn't link to anything

for more infos -> for more information.

Marius1311 commented on 2023-06-13T15:47:47Z ----------------------------------------------------------------

done.

review-notebook-app[bot] commented 1 year ago

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michalk8 commented on 2023-06-13T01:10:40Z ----------------------------------------------------------------

When mentioning PETSc/SLEPc, would consider adding the conda install -c conda-forge petsc4py slepc4py

Please don't hardcode the link to installation instructions, use the proper {doc}.

Marius1311 commented on 2023-06-13T15:50:48Z ----------------------------------------------------------------

ok, done

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michalk8 commented on 2023-06-13T01:10:42Z ----------------------------------------------------------------

"we use the ... method to identify the terminal states."

Marius1311 commented on 2023-06-13T15:51:24Z ----------------------------------------------------------------

ok.

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michalk8 commented on 2023-06-13T01:10:43Z ----------------------------------------------------------------

continious -> continuous

Marius1311 commented on 2023-06-13T15:52:01Z ----------------------------------------------------------------

ok, done.

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michalk8 commented on 2023-06-13T01:10:44Z ----------------------------------------------------------------

Maybe mention higher intensity/saturation means higher certainty.

Marius1311 commented on 2023-06-13T15:54:18Z ----------------------------------------------------------------

done.

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michalk8 commented on 2023-06-13T01:10:45Z ----------------------------------------------------------------

states using the {meth}... method.

Marius1311 commented on 2023-06-13T15:55:41Z ----------------------------------------------------------------

done.

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michalk8 commented on 2023-06-13T01:10:46Z ----------------------------------------------------------------

"and can be inspected conveniently."

I'd have expected you should g.initial_states and g.terminal_states

Marius1311 commented on 2023-06-13T16:01:44Z ----------------------------------------------------------------

Ok, I added that.

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michalk8 commented on 2023-06-13T01:10:47Z ----------------------------------------------------------------

inintial -> initial

Marius1311 commented on 2023-06-13T16:02:45Z ----------------------------------------------------------------

thanks.

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michalk8 commented on 2023-06-13T01:10:48Z ----------------------------------------------------------------

initial- -> initial

Marius1311 commented on 2023-06-13T16:03:01Z ----------------------------------------------------------------

done.

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michalk8 commented on 2023-06-13T01:10:49Z ----------------------------------------------------------------

Would not use italics for terminal.

knowlege -> knowledge

which we show below -> as shown below.

Marius1311 commented on 2023-06-13T16:03:44Z ----------------------------------------------------------------

ok.

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michalk8 commented on 2023-06-13T01:10:50Z ----------------------------------------------------------------

probabilits -> probability

Marius1311 commented on 2023-06-13T16:04:09Z ----------------------------------------------------------------

done.

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michalk8 commented on 2023-06-13T01:10:51Z ----------------------------------------------------------------

we compute the macrostates.

dashed vertical line

Marius1311 commented on 2023-06-13T16:04:49Z ----------------------------------------------------------------

ok.

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michalk8 commented on 2023-06-13T01:10:52Z ----------------------------------------------------------------

Remove the Nice!

...; however, that does -> . However, that does not

Missing . in the last sentence.

; we show below -> . We show below

" for each of the cells most confidently assigned to a certain macrostates" reads not so easily

Marius1311 commented on 2023-06-13T16:06:30Z ----------------------------------------------------------------

thanks, done

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michalk8 commented on 2023-06-13T01:10:53Z ----------------------------------------------------------------

any {attr}... -> any observation-level covariate

Link to the transport map kernel tutorial rather than the class (or both) (also missing the {class} role for the kernel).

Marius1311 commented on 2023-06-13T16:09:29Z ----------------------------------------------------------------

done.

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michalk8 commented on 2023-06-13T01:10:54Z ----------------------------------------------------------------

becasue -> because

Let's try the automatic terminal

Marius1311 commented on 2023-06-13T16:10:54Z ----------------------------------------------------------------

done.

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michalk8 commented on 2023-06-13T01:10:54Z ----------------------------------------------------------------

ductal-cell markers -> Ductal cell markers.

Marius1311 commented on 2023-06-13T16:11:44Z ----------------------------------------------------------------

done.

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michalk8 commented on 2023-06-13T01:10:55Z ----------------------------------------------------------------

as initial -> as an initial state.

Marius1311 commented on 2023-06-13T16:12:02Z ----------------------------------------------------------------

ok.

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michalk8 commented on 2023-06-13T01:10:56Z ----------------------------------------------------------------

we recommend... -> we recommend to: + go thrgouh/take a look/take a look/

Marius1311 commented on 2023-06-13T16:12:46Z ----------------------------------------------------------------

thanks!

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michalk8 commented on 2023-06-13T01:15:06Z ----------------------------------------------------------------

{attr) -> {attr}

Marius1311 commented on 2023-06-13T16:10:10Z ----------------------------------------------------------------

done.

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michalk8 commented on 2023-06-13T01:15:07Z ----------------------------------------------------------------

compute the {attr}fate probabilities <...> .

Marius1311 commented on 2023-06-13T16:11:19Z ----------------------------------------------------------------

done.

Marius1311 commented 1 year ago

makes sense. I moved it.

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Marius1311 commented 1 year ago

yes, I'll change this everywhere.

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Marius1311 commented 1 year ago

ok.

---

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Marius1311 commented 1 year ago

done.

---

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Marius1311 commented 1 year ago

I moved it to the first paragraph.

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Marius1311 commented 1 year ago

ok, adapted.

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Marius1311 commented 1 year ago

done, thanks!

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Marius1311 commented 1 year ago

ok.

---

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Marius1311 commented 1 year ago

well...

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Marius1311 commented 1 year ago

ok, done.

---

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Marius1311 commented 1 year ago

I removed these from the section heading.

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Marius1311 commented 1 year ago

included already (reuter:22)

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Marius1311 commented 1 year ago

you're right, that seems to be the case. adapted.

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michalk8 commented on 2023-06-13T01:10:39Z ----------------------------------------------------------------

Can we please remove the horizontal and vertical lines + fix the figure aspect ratio?

Marius1311 commented on 2023-06-13T15:46:12Z ----------------------------------------------------------------

I don't know how

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michalk8 commented on 2023-06-13T01:10:40Z ----------------------------------------------------------------

adata.obs['clusters'] -> {attr}adata.obs['clusters'] <anndata.AnnData.obs>.

{mod}pyGPCCA doesn't link to anything

for more infos -> for more information.

Marius1311 commented on 2023-06-13T15:47:47Z ----------------------------------------------------------------

done.

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michalk8 commented on 2023-06-13T01:10:40Z ----------------------------------------------------------------

When mentioning PETSc/SLEPc, would consider adding the conda install -c conda-forge petsc4py slepc4py

Please don't hardcode the link to installation instructions, use the proper {doc}.

Marius1311 commented on 2023-06-13T15:50:48Z ----------------------------------------------------------------

ok, done

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michalk8 commented on 2023-06-13T01:10:42Z ----------------------------------------------------------------

"we use the ... method to identify the terminal states."

Marius1311 commented on 2023-06-13T15:51:24Z ----------------------------------------------------------------

ok.

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michalk8 commented on 2023-06-13T01:10:43Z ----------------------------------------------------------------

continious -> continuous

Marius1311 commented on 2023-06-13T15:52:01Z ----------------------------------------------------------------

ok, done.

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michalk8 commented on 2023-06-13T01:10:44Z ----------------------------------------------------------------

Maybe mention higher intensity/saturation means higher certainty.

Marius1311 commented on 2023-06-13T15:54:18Z ----------------------------------------------------------------

done.

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michalk8 commented on 2023-06-13T01:10:45Z ----------------------------------------------------------------

states using the {meth}... method.

Marius1311 commented on 2023-06-13T15:55:41Z ----------------------------------------------------------------

done.

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michalk8 commented on 2023-06-13T01:10:46Z ----------------------------------------------------------------

"and can be inspected conveniently."

I'd have expected you should g.initial_states and g.terminal_states

Marius1311 commented on 2023-06-13T16:01:44Z ----------------------------------------------------------------

Ok, I added that.

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michalk8 commented on 2023-06-13T01:10:47Z ----------------------------------------------------------------

inintial -> initial

Marius1311 commented on 2023-06-13T16:02:45Z ----------------------------------------------------------------

thanks.

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michalk8 commented on 2023-06-13T01:10:48Z ----------------------------------------------------------------

initial- -> initial

Marius1311 commented on 2023-06-13T16:03:01Z ----------------------------------------------------------------

done.

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michalk8 commented on 2023-06-13T01:10:49Z ----------------------------------------------------------------

Would not use italics for terminal.

knowlege -> knowledge

which we show below -> as shown below.

Marius1311 commented on 2023-06-13T16:03:44Z ----------------------------------------------------------------

ok.

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michalk8 commented on 2023-06-13T01:10:50Z ----------------------------------------------------------------

probabilits -> probability

Marius1311 commented on 2023-06-13T16:04:09Z ----------------------------------------------------------------

done.

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michalk8 commented on 2023-06-13T01:10:51Z ----------------------------------------------------------------

we compute the macrostates.

dashed vertical line

Marius1311 commented on 2023-06-13T16:04:49Z ----------------------------------------------------------------

ok.

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michalk8 commented on 2023-06-13T01:10:52Z ----------------------------------------------------------------

Remove the Nice!

...; however, that does -> . However, that does not

Missing . in the last sentence.

; we show below -> . We show below

" for each of the cells most confidently assigned to a certain macrostates" reads not so easily

Marius1311 commented on 2023-06-13T16:06:30Z ----------------------------------------------------------------

thanks, done

review-notebook-app[bot] commented 1 year ago

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michalk8 commented on 2023-06-13T01:10:53Z ----------------------------------------------------------------

any {attr}... -> any observation-level covariate

Link to the transport map kernel tutorial rather than the class (or both) (also missing the {class} role for the kernel).

Marius1311 commented on 2023-06-13T16:09:29Z ----------------------------------------------------------------

done.

review-notebook-app[bot] commented 1 year ago

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michalk8 commented on 2023-06-13T01:10:54Z ----------------------------------------------------------------

becasue -> because

Let's try the automatic terminal

Marius1311 commented on 2023-06-13T16:10:54Z ----------------------------------------------------------------

done.

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michalk8 commented on 2023-06-13T01:10:54Z ----------------------------------------------------------------

ductal-cell markers -> Ductal cell markers.

Marius1311 commented on 2023-06-13T16:11:44Z ----------------------------------------------------------------

done.

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michalk8 commented on 2023-06-13T01:10:55Z ----------------------------------------------------------------

as initial -> as an initial state.

Marius1311 commented on 2023-06-13T16:12:02Z ----------------------------------------------------------------

ok.

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michalk8 commented on 2023-06-13T01:10:56Z ----------------------------------------------------------------

we recommend... -> we recommend to: + go thrgouh/take a look/take a look/

Marius1311 commented on 2023-06-13T16:12:46Z ----------------------------------------------------------------

thanks!

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michalk8 commented on 2023-06-13T01:15:06Z ----------------------------------------------------------------

{attr) -> {attr}

Marius1311 commented on 2023-06-13T16:10:10Z ----------------------------------------------------------------

done.

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michalk8 commented on 2023-06-13T01:15:07Z ----------------------------------------------------------------

compute the {attr}fate probabilities <...> .

Marius1311 commented on 2023-06-13T16:11:19Z ----------------------------------------------------------------

done.

Marius1311 commented 1 year ago

makes sense. I moved it.

---

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Marius1311 commented 1 year ago

yes, I'll change this everywhere.

---

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Marius1311 commented 1 year ago

ok.

---

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Marius1311 commented 1 year ago

done.

---

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Marius1311 commented 1 year ago

I moved it to the first paragraph.

---

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Marius1311 commented 1 year ago

ok, adapted.

---

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Marius1311 commented 1 year ago

done, thanks!

---

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Marius1311 commented 1 year ago

ok.

---

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Marius1311 commented 1 year ago

well...

---

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Marius1311 commented 1 year ago

ok, done.

---

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Marius1311 commented 1 year ago

I removed these from the section heading.

---

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Marius1311 commented 1 year ago

included already (reuter:22)

---

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Marius1311 commented 1 year ago

you're right, that seems to be the case. adapted.

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michalk8 commented on 2023-06-13T01:10:40Z ----------------------------------------------------------------

adata.obs['clusters'] -> {attr}adata.obs['clusters'] <anndata.AnnData.obs>.

{mod}pyGPCCA doesn't link to anything

for more infos -> for more information.

Marius1311 commented on 2023-06-13T15:47:47Z ----------------------------------------------------------------

done.

review-notebook-app[bot] commented 1 year ago

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michalk8 commented on 2023-06-13T01:10:40Z ----------------------------------------------------------------

When mentioning PETSc/SLEPc, would consider adding the conda install -c conda-forge petsc4py slepc4py

Please don't hardcode the link to installation instructions, use the proper {doc}.

Marius1311 commented on 2023-06-13T15:50:48Z ----------------------------------------------------------------

ok, done

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michalk8 commented on 2023-06-13T01:10:42Z ----------------------------------------------------------------

"we use the ... method to identify the terminal states."

Marius1311 commented on 2023-06-13T15:51:24Z ----------------------------------------------------------------

ok.

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michalk8 commented on 2023-06-13T01:10:43Z ----------------------------------------------------------------

continious -> continuous

Marius1311 commented on 2023-06-13T15:52:01Z ----------------------------------------------------------------

ok, done.

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michalk8 commented on 2023-06-13T01:10:44Z ----------------------------------------------------------------

Maybe mention higher intensity/saturation means higher certainty.

Marius1311 commented on 2023-06-13T15:54:18Z ----------------------------------------------------------------

done.

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michalk8 commented on 2023-06-13T01:10:45Z ----------------------------------------------------------------

states using the {meth}... method.

Marius1311 commented on 2023-06-13T15:55:41Z ----------------------------------------------------------------

done.

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michalk8 commented on 2023-06-13T01:10:46Z ----------------------------------------------------------------

"and can be inspected conveniently."

I'd have expected you should g.initial_states and g.terminal_states

Marius1311 commented on 2023-06-13T16:01:44Z ----------------------------------------------------------------

Ok, I added that.

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michalk8 commented on 2023-06-13T01:10:47Z ----------------------------------------------------------------

inintial -> initial

Marius1311 commented on 2023-06-13T16:02:45Z ----------------------------------------------------------------

thanks.

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michalk8 commented on 2023-06-13T01:10:48Z ----------------------------------------------------------------

initial- -> initial

Marius1311 commented on 2023-06-13T16:03:01Z ----------------------------------------------------------------

done.

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michalk8 commented on 2023-06-13T01:10:49Z ----------------------------------------------------------------

Would not use italics for terminal.

knowlege -> knowledge

which we show below -> as shown below.

Marius1311 commented on 2023-06-13T16:03:44Z ----------------------------------------------------------------

ok.

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michalk8 commented on 2023-06-13T01:10:50Z ----------------------------------------------------------------

probabilits -> probability

Marius1311 commented on 2023-06-13T16:04:09Z ----------------------------------------------------------------

done.

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michalk8 commented on 2023-06-13T01:10:51Z ----------------------------------------------------------------

we compute the macrostates.

dashed vertical line

Marius1311 commented on 2023-06-13T16:04:49Z ----------------------------------------------------------------

ok.

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michalk8 commented on 2023-06-13T01:10:52Z ----------------------------------------------------------------

Remove the Nice!

...; however, that does -> . However, that does not

Missing . in the last sentence.

; we show below -> . We show below

" for each of the cells most confidently assigned to a certain macrostates" reads not so easily

Marius1311 commented on 2023-06-13T16:06:30Z ----------------------------------------------------------------

thanks, done

review-notebook-app[bot] commented 1 year ago

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michalk8 commented on 2023-06-13T01:10:53Z ----------------------------------------------------------------

any {attr}... -> any observation-level covariate

Link to the transport map kernel tutorial rather than the class (or both) (also missing the {class} role for the kernel).

Marius1311 commented on 2023-06-13T16:09:29Z ----------------------------------------------------------------

done.

review-notebook-app[bot] commented 1 year ago

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michalk8 commented on 2023-06-13T01:10:54Z ----------------------------------------------------------------

becasue -> because

Let's try the automatic terminal

Marius1311 commented on 2023-06-13T16:10:54Z ----------------------------------------------------------------

done.

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michalk8 commented on 2023-06-13T01:10:54Z ----------------------------------------------------------------

ductal-cell markers -> Ductal cell markers.

Marius1311 commented on 2023-06-13T16:11:44Z ----------------------------------------------------------------

done.

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michalk8 commented on 2023-06-13T01:10:55Z ----------------------------------------------------------------

as initial -> as an initial state.

Marius1311 commented on 2023-06-13T16:12:02Z ----------------------------------------------------------------

ok.

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michalk8 commented on 2023-06-13T01:10:56Z ----------------------------------------------------------------

we recommend... -> we recommend to: + go thrgouh/take a look/take a look/

Marius1311 commented on 2023-06-13T16:12:46Z ----------------------------------------------------------------

thanks!

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michalk8 commented on 2023-06-13T01:15:06Z ----------------------------------------------------------------

{attr) -> {attr}

Marius1311 commented on 2023-06-13T16:10:10Z ----------------------------------------------------------------

done.

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michalk8 commented on 2023-06-13T01:15:07Z ----------------------------------------------------------------

compute the {attr}fate probabilities <...> .

Marius1311 commented on 2023-06-13T16:11:19Z ----------------------------------------------------------------

done.

Marius1311 commented 1 year ago

makes sense. I moved it.

---

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Marius1311 commented 1 year ago

yes, I'll change this everywhere.

---

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Marius1311 commented 1 year ago

ok.

---

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Marius1311 commented 1 year ago

done.

---

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Marius1311 commented 1 year ago

I moved it to the first paragraph.

---

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Marius1311 commented 1 year ago

ok, adapted.

---

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Marius1311 commented 1 year ago

done, thanks!

---

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Marius1311 commented 1 year ago

ok.

---

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Marius1311 commented 1 year ago

well...

---

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Marius1311 commented 1 year ago

ok, done.

---

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Marius1311 commented 1 year ago

I removed these from the section heading.

---

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Marius1311 commented 1 year ago

included already (reuter:22)

---

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Marius1311 commented 1 year ago

you're right, that seems to be the case. adapted.

---

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michalk8 commented on 2023-06-13T01:10:40Z ----------------------------------------------------------------

When mentioning PETSc/SLEPc, would consider adding the conda install -c conda-forge petsc4py slepc4py

Please don't hardcode the link to installation instructions, use the proper {doc}.

Marius1311 commented on 2023-06-13T15:50:48Z ----------------------------------------------------------------

ok, done

review-notebook-app[bot] commented 1 year ago

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michalk8 commented on 2023-06-13T01:10:42Z ----------------------------------------------------------------

"we use the ... method to identify the terminal states."

Marius1311 commented on 2023-06-13T15:51:24Z ----------------------------------------------------------------

ok.

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michalk8 commented on 2023-06-13T01:10:43Z ----------------------------------------------------------------

continious -> continuous

Marius1311 commented on 2023-06-13T15:52:01Z ----------------------------------------------------------------

ok, done.

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michalk8 commented on 2023-06-13T01:10:44Z ----------------------------------------------------------------

Maybe mention higher intensity/saturation means higher certainty.

Marius1311 commented on 2023-06-13T15:54:18Z ----------------------------------------------------------------

done.

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michalk8 commented on 2023-06-13T01:10:45Z ----------------------------------------------------------------

states using the {meth}... method.

Marius1311 commented on 2023-06-13T15:55:41Z ----------------------------------------------------------------

done.

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michalk8 commented on 2023-06-13T01:10:46Z ----------------------------------------------------------------

"and can be inspected conveniently."

I'd have expected you should g.initial_states and g.terminal_states

Marius1311 commented on 2023-06-13T16:01:44Z ----------------------------------------------------------------

Ok, I added that.

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michalk8 commented on 2023-06-13T01:10:47Z ----------------------------------------------------------------

inintial -> initial

Marius1311 commented on 2023-06-13T16:02:45Z ----------------------------------------------------------------

thanks.

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michalk8 commented on 2023-06-13T01:10:48Z ----------------------------------------------------------------

initial- -> initial

Marius1311 commented on 2023-06-13T16:03:01Z ----------------------------------------------------------------

done.

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michalk8 commented on 2023-06-13T01:10:49Z ----------------------------------------------------------------

Would not use italics for terminal.

knowlege -> knowledge

which we show below -> as shown below.

Marius1311 commented on 2023-06-13T16:03:44Z ----------------------------------------------------------------

ok.

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michalk8 commented on 2023-06-13T01:10:50Z ----------------------------------------------------------------

probabilits -> probability

Marius1311 commented on 2023-06-13T16:04:09Z ----------------------------------------------------------------

done.

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michalk8 commented on 2023-06-13T01:10:51Z ----------------------------------------------------------------

we compute the macrostates.

dashed vertical line

Marius1311 commented on 2023-06-13T16:04:49Z ----------------------------------------------------------------

ok.

review-notebook-app[bot] commented 1 year ago

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michalk8 commented on 2023-06-13T01:10:52Z ----------------------------------------------------------------

Remove the Nice!

...; however, that does -> . However, that does not

Missing . in the last sentence.

; we show below -> . We show below

" for each of the cells most confidently assigned to a certain macrostates" reads not so easily

Marius1311 commented on 2023-06-13T16:06:30Z ----------------------------------------------------------------

thanks, done

review-notebook-app[bot] commented 1 year ago

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michalk8 commented on 2023-06-13T01:10:53Z ----------------------------------------------------------------

any {attr}... -> any observation-level covariate

Link to the transport map kernel tutorial rather than the class (or both) (also missing the {class} role for the kernel).

Marius1311 commented on 2023-06-13T16:09:29Z ----------------------------------------------------------------

done.

review-notebook-app[bot] commented 1 year ago

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michalk8 commented on 2023-06-13T01:10:54Z ----------------------------------------------------------------

becasue -> because

Let's try the automatic terminal

Marius1311 commented on 2023-06-13T16:10:54Z ----------------------------------------------------------------

done.

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michalk8 commented on 2023-06-13T01:10:54Z ----------------------------------------------------------------

ductal-cell markers -> Ductal cell markers.

Marius1311 commented on 2023-06-13T16:11:44Z ----------------------------------------------------------------

done.

review-notebook-app[bot] commented 1 year ago

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michalk8 commented on 2023-06-13T01:10:55Z ----------------------------------------------------------------

as initial -> as an initial state.

Marius1311 commented on 2023-06-13T16:12:02Z ----------------------------------------------------------------

ok.

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michalk8 commented on 2023-06-13T01:10:56Z ----------------------------------------------------------------

we recommend... -> we recommend to: + go thrgouh/take a look/take a look/

Marius1311 commented on 2023-06-13T16:12:46Z ----------------------------------------------------------------

thanks!

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michalk8 commented on 2023-06-13T01:15:06Z ----------------------------------------------------------------

{attr) -> {attr}

Marius1311 commented on 2023-06-13T16:10:10Z ----------------------------------------------------------------

done.

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michalk8 commented on 2023-06-13T01:15:07Z ----------------------------------------------------------------

compute the {attr}fate probabilities <...> .

Marius1311 commented on 2023-06-13T16:11:19Z ----------------------------------------------------------------

done.

Marius1311 commented 1 year ago

makes sense. I moved it.

---

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Marius1311 commented 1 year ago

yes, I'll change this everywhere.

---

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Marius1311 commented 1 year ago

ok.

---

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Marius1311 commented 1 year ago

done.

---

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Marius1311 commented 1 year ago

I moved it to the first paragraph.

---

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Marius1311 commented 1 year ago

ok, adapted.

---

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Marius1311 commented 1 year ago

done, thanks!

---

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Marius1311 commented 1 year ago

ok.

---

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Marius1311 commented 1 year ago

well...

---

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Marius1311 commented 1 year ago

ok, done.

---

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Marius1311 commented 1 year ago

I removed these from the section heading.

---

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Marius1311 commented 1 year ago

included already (reuter:22)

---

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Marius1311 commented 1 year ago

you're right, that seems to be the case. adapted.

---

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michalk8 commented on 2023-06-13T01:10:42Z ----------------------------------------------------------------

"we use the ... method to identify the terminal states."

Marius1311 commented on 2023-06-13T15:51:24Z ----------------------------------------------------------------

ok.

review-notebook-app[bot] commented 1 year ago

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michalk8 commented on 2023-06-13T01:10:43Z ----------------------------------------------------------------

continious -> continuous

Marius1311 commented on 2023-06-13T15:52:01Z ----------------------------------------------------------------

ok, done.

review-notebook-app[bot] commented 1 year ago

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michalk8 commented on 2023-06-13T01:10:44Z ----------------------------------------------------------------

Maybe mention higher intensity/saturation means higher certainty.

Marius1311 commented on 2023-06-13T15:54:18Z ----------------------------------------------------------------

done.

review-notebook-app[bot] commented 1 year ago

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michalk8 commented on 2023-06-13T01:10:45Z ----------------------------------------------------------------

states using the {meth}... method.

Marius1311 commented on 2023-06-13T15:55:41Z ----------------------------------------------------------------

done.

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michalk8 commented on 2023-06-13T01:10:46Z ----------------------------------------------------------------

"and can be inspected conveniently."

I'd have expected you should g.initial_states and g.terminal_states

Marius1311 commented on 2023-06-13T16:01:44Z ----------------------------------------------------------------

Ok, I added that.

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michalk8 commented on 2023-06-13T01:10:47Z ----------------------------------------------------------------

inintial -> initial

Marius1311 commented on 2023-06-13T16:02:45Z ----------------------------------------------------------------

thanks.

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michalk8 commented on 2023-06-13T01:10:48Z ----------------------------------------------------------------

initial- -> initial

Marius1311 commented on 2023-06-13T16:03:01Z ----------------------------------------------------------------

done.

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michalk8 commented on 2023-06-13T01:10:49Z ----------------------------------------------------------------

Would not use italics for terminal.

knowlege -> knowledge

which we show below -> as shown below.

Marius1311 commented on 2023-06-13T16:03:44Z ----------------------------------------------------------------

ok.

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michalk8 commented on 2023-06-13T01:10:50Z ----------------------------------------------------------------

probabilits -> probability

Marius1311 commented on 2023-06-13T16:04:09Z ----------------------------------------------------------------

done.

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michalk8 commented on 2023-06-13T01:10:51Z ----------------------------------------------------------------

we compute the macrostates.

dashed vertical line

Marius1311 commented on 2023-06-13T16:04:49Z ----------------------------------------------------------------

ok.

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michalk8 commented on 2023-06-13T01:10:52Z ----------------------------------------------------------------

Remove the Nice!

...; however, that does -> . However, that does not

Missing . in the last sentence.

; we show below -> . We show below

" for each of the cells most confidently assigned to a certain macrostates" reads not so easily

Marius1311 commented on 2023-06-13T16:06:30Z ----------------------------------------------------------------

thanks, done

review-notebook-app[bot] commented 1 year ago

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michalk8 commented on 2023-06-13T01:10:53Z ----------------------------------------------------------------

any {attr}... -> any observation-level covariate

Link to the transport map kernel tutorial rather than the class (or both) (also missing the {class} role for the kernel).

Marius1311 commented on 2023-06-13T16:09:29Z ----------------------------------------------------------------

done.

review-notebook-app[bot] commented 1 year ago

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michalk8 commented on 2023-06-13T01:10:54Z ----------------------------------------------------------------

becasue -> because

Let's try the automatic terminal

Marius1311 commented on 2023-06-13T16:10:54Z ----------------------------------------------------------------

done.

review-notebook-app[bot] commented 1 year ago

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michalk8 commented on 2023-06-13T01:10:54Z ----------------------------------------------------------------

ductal-cell markers -> Ductal cell markers.

Marius1311 commented on 2023-06-13T16:11:44Z ----------------------------------------------------------------

done.

review-notebook-app[bot] commented 1 year ago

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michalk8 commented on 2023-06-13T01:10:55Z ----------------------------------------------------------------

as initial -> as an initial state.

Marius1311 commented on 2023-06-13T16:12:02Z ----------------------------------------------------------------

ok.

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michalk8 commented on 2023-06-13T01:10:56Z ----------------------------------------------------------------

we recommend... -> we recommend to: + go thrgouh/take a look/take a look/

Marius1311 commented on 2023-06-13T16:12:46Z ----------------------------------------------------------------

thanks!

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michalk8 commented on 2023-06-13T01:15:06Z ----------------------------------------------------------------

{attr) -> {attr}

Marius1311 commented on 2023-06-13T16:10:10Z ----------------------------------------------------------------

done.

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michalk8 commented on 2023-06-13T01:15:07Z ----------------------------------------------------------------

compute the {attr}fate probabilities <...> .

Marius1311 commented on 2023-06-13T16:11:19Z ----------------------------------------------------------------

done.

Marius1311 commented 1 year ago

makes sense. I moved it.

---

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Marius1311 commented 1 year ago

yes, I'll change this everywhere.

---

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Marius1311 commented 1 year ago

ok.

---

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Marius1311 commented 1 year ago

done.

---

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Marius1311 commented 1 year ago

I moved it to the first paragraph.

---

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Marius1311 commented 1 year ago

ok, adapted.

---

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Marius1311 commented 1 year ago

done, thanks!

---

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Marius1311 commented 1 year ago

ok.

---

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Marius1311 commented 1 year ago

well...

---

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Marius1311 commented 1 year ago

ok, done.

---

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Marius1311 commented 1 year ago

I removed these from the section heading.

---

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Marius1311 commented 1 year ago

included already (reuter:22)

---

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Marius1311 commented 1 year ago

you're right, that seems to be the case. adapted.

---

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michalk8 commented on 2023-06-13T01:10:43Z ----------------------------------------------------------------

continious -> continuous

Marius1311 commented on 2023-06-13T15:52:01Z ----------------------------------------------------------------

ok, done.

review-notebook-app[bot] commented 1 year ago

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michalk8 commented on 2023-06-13T01:10:44Z ----------------------------------------------------------------

Maybe mention higher intensity/saturation means higher certainty.

Marius1311 commented on 2023-06-13T15:54:18Z ----------------------------------------------------------------

done.

review-notebook-app[bot] commented 1 year ago

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michalk8 commented on 2023-06-13T01:10:45Z ----------------------------------------------------------------

states using the {meth}... method.

Marius1311 commented on 2023-06-13T15:55:41Z ----------------------------------------------------------------

done.

review-notebook-app[bot] commented 1 year ago

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michalk8 commented on 2023-06-13T01:10:46Z ----------------------------------------------------------------

"and can be inspected conveniently."

I'd have expected you should g.initial_states and g.terminal_states

Marius1311 commented on 2023-06-13T16:01:44Z ----------------------------------------------------------------

Ok, I added that.

review-notebook-app[bot] commented 1 year ago

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michalk8 commented on 2023-06-13T01:10:47Z ----------------------------------------------------------------

inintial -> initial

Marius1311 commented on 2023-06-13T16:02:45Z ----------------------------------------------------------------

thanks.

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michalk8 commented on 2023-06-13T01:10:48Z ----------------------------------------------------------------

initial- -> initial

Marius1311 commented on 2023-06-13T16:03:01Z ----------------------------------------------------------------

done.

review-notebook-app[bot] commented 1 year ago

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michalk8 commented on 2023-06-13T01:10:49Z ----------------------------------------------------------------

Would not use italics for terminal.

knowlege -> knowledge

which we show below -> as shown below.

Marius1311 commented on 2023-06-13T16:03:44Z ----------------------------------------------------------------

ok.

review-notebook-app[bot] commented 1 year ago

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michalk8 commented on 2023-06-13T01:10:50Z ----------------------------------------------------------------

probabilits -> probability

Marius1311 commented on 2023-06-13T16:04:09Z ----------------------------------------------------------------

done.

review-notebook-app[bot] commented 1 year ago

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michalk8 commented on 2023-06-13T01:10:51Z ----------------------------------------------------------------

we compute the macrostates.

dashed vertical line

Marius1311 commented on 2023-06-13T16:04:49Z ----------------------------------------------------------------

ok.

review-notebook-app[bot] commented 1 year ago

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michalk8 commented on 2023-06-13T01:10:52Z ----------------------------------------------------------------

Remove the Nice!

...; however, that does -> . However, that does not

Missing . in the last sentence.

; we show below -> . We show below

" for each of the cells most confidently assigned to a certain macrostates" reads not so easily

Marius1311 commented on 2023-06-13T16:06:30Z ----------------------------------------------------------------

thanks, done

review-notebook-app[bot] commented 1 year ago

View / edit / reply to this conversation on ReviewNB

michalk8 commented on 2023-06-13T01:10:53Z ----------------------------------------------------------------

any {attr}... -> any observation-level covariate

Link to the transport map kernel tutorial rather than the class (or both) (also missing the {class} role for the kernel).

Marius1311 commented on 2023-06-13T16:09:29Z ----------------------------------------------------------------

done.

review-notebook-app[bot] commented 1 year ago

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michalk8 commented on 2023-06-13T01:10:54Z ----------------------------------------------------------------

becasue -> because

Let's try the automatic terminal

Marius1311 commented on 2023-06-13T16:10:54Z ----------------------------------------------------------------

done.

review-notebook-app[bot] commented 1 year ago

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michalk8 commented on 2023-06-13T01:10:54Z ----------------------------------------------------------------

ductal-cell markers -> Ductal cell markers.

Marius1311 commented on 2023-06-13T16:11:44Z ----------------------------------------------------------------

done.

review-notebook-app[bot] commented 1 year ago

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michalk8 commented on 2023-06-13T01:10:55Z ----------------------------------------------------------------

as initial -> as an initial state.

Marius1311 commented on 2023-06-13T16:12:02Z ----------------------------------------------------------------

ok.

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michalk8 commented on 2023-06-13T01:10:56Z ----------------------------------------------------------------

we recommend... -> we recommend to: + go thrgouh/take a look/take a look/

Marius1311 commented on 2023-06-13T16:12:46Z ----------------------------------------------------------------

thanks!

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michalk8 commented on 2023-06-13T01:15:06Z ----------------------------------------------------------------

{attr) -> {attr}

Marius1311 commented on 2023-06-13T16:10:10Z ----------------------------------------------------------------

done.

review-notebook-app[bot] commented 1 year ago

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michalk8 commented on 2023-06-13T01:15:07Z ----------------------------------------------------------------

compute the {attr}fate probabilities <...> .

Marius1311 commented on 2023-06-13T16:11:19Z ----------------------------------------------------------------

done.

Marius1311 commented 1 year ago

makes sense. I moved it.

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

yes, I'll change this everywhere.

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

ok.

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

done.

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

I moved it to the first paragraph.

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

ok, adapted.

---

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Marius1311 commented 1 year ago

done, thanks!

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

ok.

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

well...

---

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Marius1311 commented 1 year ago

ok, done.

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

I removed these from the section heading.

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

included already (reuter:22)

---

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Marius1311 commented 1 year ago

you're right, that seems to be the case. adapted.

---

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michalk8 commented on 2023-06-13T01:10:44Z ----------------------------------------------------------------

Maybe mention higher intensity/saturation means higher certainty.

Marius1311 commented on 2023-06-13T15:54:18Z ----------------------------------------------------------------

done.

review-notebook-app[bot] commented 1 year ago

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michalk8 commented on 2023-06-13T01:10:45Z ----------------------------------------------------------------

states using the {meth}... method.

Marius1311 commented on 2023-06-13T15:55:41Z ----------------------------------------------------------------

done.

review-notebook-app[bot] commented 1 year ago

View / edit / reply to this conversation on ReviewNB

michalk8 commented on 2023-06-13T01:10:46Z ----------------------------------------------------------------

"and can be inspected conveniently."

I'd have expected you should g.initial_states and g.terminal_states

Marius1311 commented on 2023-06-13T16:01:44Z ----------------------------------------------------------------

Ok, I added that.

review-notebook-app[bot] commented 1 year ago

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michalk8 commented on 2023-06-13T01:10:47Z ----------------------------------------------------------------

inintial -> initial

Marius1311 commented on 2023-06-13T16:02:45Z ----------------------------------------------------------------

thanks.

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michalk8 commented on 2023-06-13T01:10:48Z ----------------------------------------------------------------

initial- -> initial

Marius1311 commented on 2023-06-13T16:03:01Z ----------------------------------------------------------------

done.

review-notebook-app[bot] commented 1 year ago

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michalk8 commented on 2023-06-13T01:10:49Z ----------------------------------------------------------------

Would not use italics for terminal.

knowlege -> knowledge

which we show below -> as shown below.

Marius1311 commented on 2023-06-13T16:03:44Z ----------------------------------------------------------------

ok.

review-notebook-app[bot] commented 1 year ago

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michalk8 commented on 2023-06-13T01:10:50Z ----------------------------------------------------------------

probabilits -> probability

Marius1311 commented on 2023-06-13T16:04:09Z ----------------------------------------------------------------

done.

review-notebook-app[bot] commented 1 year ago

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michalk8 commented on 2023-06-13T01:10:51Z ----------------------------------------------------------------

we compute the macrostates.

dashed vertical line

Marius1311 commented on 2023-06-13T16:04:49Z ----------------------------------------------------------------

ok.

review-notebook-app[bot] commented 1 year ago

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michalk8 commented on 2023-06-13T01:10:52Z ----------------------------------------------------------------

Remove the Nice!

...; however, that does -> . However, that does not

Missing . in the last sentence.

; we show below -> . We show below

" for each of the cells most confidently assigned to a certain macrostates" reads not so easily

Marius1311 commented on 2023-06-13T16:06:30Z ----------------------------------------------------------------

thanks, done

review-notebook-app[bot] commented 1 year ago

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michalk8 commented on 2023-06-13T01:10:53Z ----------------------------------------------------------------

any {attr}... -> any observation-level covariate

Link to the transport map kernel tutorial rather than the class (or both) (also missing the {class} role for the kernel).

Marius1311 commented on 2023-06-13T16:09:29Z ----------------------------------------------------------------

done.

review-notebook-app[bot] commented 1 year ago

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michalk8 commented on 2023-06-13T01:10:54Z ----------------------------------------------------------------

becasue -> because

Let's try the automatic terminal

Marius1311 commented on 2023-06-13T16:10:54Z ----------------------------------------------------------------

done.

review-notebook-app[bot] commented 1 year ago

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michalk8 commented on 2023-06-13T01:10:54Z ----------------------------------------------------------------

ductal-cell markers -> Ductal cell markers.

Marius1311 commented on 2023-06-13T16:11:44Z ----------------------------------------------------------------

done.

review-notebook-app[bot] commented 1 year ago

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michalk8 commented on 2023-06-13T01:10:55Z ----------------------------------------------------------------

as initial -> as an initial state.

Marius1311 commented on 2023-06-13T16:12:02Z ----------------------------------------------------------------

ok.

review-notebook-app[bot] commented 1 year ago

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michalk8 commented on 2023-06-13T01:10:56Z ----------------------------------------------------------------

we recommend... -> we recommend to: + go thrgouh/take a look/take a look/

Marius1311 commented on 2023-06-13T16:12:46Z ----------------------------------------------------------------

thanks!

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michalk8 commented on 2023-06-13T01:15:06Z ----------------------------------------------------------------

{attr) -> {attr}

Marius1311 commented on 2023-06-13T16:10:10Z ----------------------------------------------------------------

done.

review-notebook-app[bot] commented 1 year ago

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michalk8 commented on 2023-06-13T01:15:07Z ----------------------------------------------------------------

compute the {attr}fate probabilities <...> .

Marius1311 commented on 2023-06-13T16:11:19Z ----------------------------------------------------------------

done.

Marius1311 commented 1 year ago

makes sense. I moved it.

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

yes, I'll change this everywhere.

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

ok.

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

done.

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

I moved it to the first paragraph.

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

ok, adapted.

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

done, thanks!

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

ok.

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

well...

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

ok, done.

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

I removed these from the section heading.

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

included already (reuter:22)

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

you're right, that seems to be the case. adapted.

---

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michalk8 commented on 2023-06-13T01:10:45Z ----------------------------------------------------------------

states using the {meth}... method.

Marius1311 commented on 2023-06-13T15:55:41Z ----------------------------------------------------------------

done.

review-notebook-app[bot] commented 1 year ago

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michalk8 commented on 2023-06-13T01:10:46Z ----------------------------------------------------------------

"and can be inspected conveniently."

I'd have expected you should g.initial_states and g.terminal_states

Marius1311 commented on 2023-06-13T16:01:44Z ----------------------------------------------------------------

Ok, I added that.

review-notebook-app[bot] commented 1 year ago

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michalk8 commented on 2023-06-13T01:10:47Z ----------------------------------------------------------------

inintial -> initial

Marius1311 commented on 2023-06-13T16:02:45Z ----------------------------------------------------------------

thanks.

review-notebook-app[bot] commented 1 year ago

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michalk8 commented on 2023-06-13T01:10:48Z ----------------------------------------------------------------

initial- -> initial

Marius1311 commented on 2023-06-13T16:03:01Z ----------------------------------------------------------------

done.

review-notebook-app[bot] commented 1 year ago

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michalk8 commented on 2023-06-13T01:10:49Z ----------------------------------------------------------------

Would not use italics for terminal.

knowlege -> knowledge

which we show below -> as shown below.

Marius1311 commented on 2023-06-13T16:03:44Z ----------------------------------------------------------------

ok.

review-notebook-app[bot] commented 1 year ago

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michalk8 commented on 2023-06-13T01:10:50Z ----------------------------------------------------------------

probabilits -> probability

Marius1311 commented on 2023-06-13T16:04:09Z ----------------------------------------------------------------

done.

review-notebook-app[bot] commented 1 year ago

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michalk8 commented on 2023-06-13T01:10:51Z ----------------------------------------------------------------

we compute the macrostates.

dashed vertical line

Marius1311 commented on 2023-06-13T16:04:49Z ----------------------------------------------------------------

ok.

review-notebook-app[bot] commented 1 year ago

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michalk8 commented on 2023-06-13T01:10:52Z ----------------------------------------------------------------

Remove the Nice!

...; however, that does -> . However, that does not

Missing . in the last sentence.

; we show below -> . We show below

" for each of the cells most confidently assigned to a certain macrostates" reads not so easily

Marius1311 commented on 2023-06-13T16:06:30Z ----------------------------------------------------------------

thanks, done

review-notebook-app[bot] commented 1 year ago

View / edit / reply to this conversation on ReviewNB

michalk8 commented on 2023-06-13T01:10:53Z ----------------------------------------------------------------

any {attr}... -> any observation-level covariate

Link to the transport map kernel tutorial rather than the class (or both) (also missing the {class} role for the kernel).

Marius1311 commented on 2023-06-13T16:09:29Z ----------------------------------------------------------------

done.

review-notebook-app[bot] commented 1 year ago

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michalk8 commented on 2023-06-13T01:10:54Z ----------------------------------------------------------------

becasue -> because

Let's try the automatic terminal

Marius1311 commented on 2023-06-13T16:10:54Z ----------------------------------------------------------------

done.

review-notebook-app[bot] commented 1 year ago

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michalk8 commented on 2023-06-13T01:10:54Z ----------------------------------------------------------------

ductal-cell markers -> Ductal cell markers.

Marius1311 commented on 2023-06-13T16:11:44Z ----------------------------------------------------------------

done.

review-notebook-app[bot] commented 1 year ago

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michalk8 commented on 2023-06-13T01:10:55Z ----------------------------------------------------------------

as initial -> as an initial state.

Marius1311 commented on 2023-06-13T16:12:02Z ----------------------------------------------------------------

ok.

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michalk8 commented on 2023-06-13T01:10:56Z ----------------------------------------------------------------

we recommend... -> we recommend to: + go thrgouh/take a look/take a look/

Marius1311 commented on 2023-06-13T16:12:46Z ----------------------------------------------------------------

thanks!

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michalk8 commented on 2023-06-13T01:15:06Z ----------------------------------------------------------------

{attr) -> {attr}

Marius1311 commented on 2023-06-13T16:10:10Z ----------------------------------------------------------------

done.

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michalk8 commented on 2023-06-13T01:15:07Z ----------------------------------------------------------------

compute the {attr}fate probabilities <...> .

Marius1311 commented on 2023-06-13T16:11:19Z ----------------------------------------------------------------

done.

Marius1311 commented 1 year ago

makes sense. I moved it.

---

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Marius1311 commented 1 year ago

yes, I'll change this everywhere.

---

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Marius1311 commented 1 year ago

ok.

---

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Marius1311 commented 1 year ago

done.

---

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Marius1311 commented 1 year ago

I moved it to the first paragraph.

---

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Marius1311 commented 1 year ago

ok, adapted.

---

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Marius1311 commented 1 year ago

done, thanks!

---

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Marius1311 commented 1 year ago

ok.

---

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Marius1311 commented 1 year ago

well...

---

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Marius1311 commented 1 year ago

ok, done.

---

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Marius1311 commented 1 year ago

I removed these from the section heading.

---

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Marius1311 commented 1 year ago

included already (reuter:22)

---

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Marius1311 commented 1 year ago

you're right, that seems to be the case. adapted.

---

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michalk8 commented on 2023-06-13T01:10:46Z ----------------------------------------------------------------

"and can be inspected conveniently."

I'd have expected you should g.initial_states and g.terminal_states

Marius1311 commented on 2023-06-13T16:01:44Z ----------------------------------------------------------------

Ok, I added that.

review-notebook-app[bot] commented 1 year ago

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michalk8 commented on 2023-06-13T01:10:47Z ----------------------------------------------------------------

inintial -> initial

Marius1311 commented on 2023-06-13T16:02:45Z ----------------------------------------------------------------

thanks.

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michalk8 commented on 2023-06-13T01:10:48Z ----------------------------------------------------------------

initial- -> initial

Marius1311 commented on 2023-06-13T16:03:01Z ----------------------------------------------------------------

done.

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michalk8 commented on 2023-06-13T01:10:49Z ----------------------------------------------------------------

Would not use italics for terminal.

knowlege -> knowledge

which we show below -> as shown below.

Marius1311 commented on 2023-06-13T16:03:44Z ----------------------------------------------------------------

ok.

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michalk8 commented on 2023-06-13T01:10:50Z ----------------------------------------------------------------

probabilits -> probability

Marius1311 commented on 2023-06-13T16:04:09Z ----------------------------------------------------------------

done.

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michalk8 commented on 2023-06-13T01:10:51Z ----------------------------------------------------------------

we compute the macrostates.

dashed vertical line

Marius1311 commented on 2023-06-13T16:04:49Z ----------------------------------------------------------------

ok.

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michalk8 commented on 2023-06-13T01:10:52Z ----------------------------------------------------------------

Remove the Nice!

...; however, that does -> . However, that does not

Missing . in the last sentence.

; we show below -> . We show below

" for each of the cells most confidently assigned to a certain macrostates" reads not so easily

Marius1311 commented on 2023-06-13T16:06:30Z ----------------------------------------------------------------

thanks, done

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michalk8 commented on 2023-06-13T01:10:53Z ----------------------------------------------------------------

any {attr}... -> any observation-level covariate

Link to the transport map kernel tutorial rather than the class (or both) (also missing the {class} role for the kernel).

Marius1311 commented on 2023-06-13T16:09:29Z ----------------------------------------------------------------

done.

review-notebook-app[bot] commented 1 year ago

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michalk8 commented on 2023-06-13T01:10:54Z ----------------------------------------------------------------

becasue -> because

Let's try the automatic terminal

Marius1311 commented on 2023-06-13T16:10:54Z ----------------------------------------------------------------

done.

review-notebook-app[bot] commented 1 year ago

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michalk8 commented on 2023-06-13T01:10:54Z ----------------------------------------------------------------

ductal-cell markers -> Ductal cell markers.

Marius1311 commented on 2023-06-13T16:11:44Z ----------------------------------------------------------------

done.

review-notebook-app[bot] commented 1 year ago

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michalk8 commented on 2023-06-13T01:10:55Z ----------------------------------------------------------------

as initial -> as an initial state.

Marius1311 commented on 2023-06-13T16:12:02Z ----------------------------------------------------------------

ok.

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michalk8 commented on 2023-06-13T01:10:56Z ----------------------------------------------------------------

we recommend... -> we recommend to: + go thrgouh/take a look/take a look/

Marius1311 commented on 2023-06-13T16:12:46Z ----------------------------------------------------------------

thanks!

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michalk8 commented on 2023-06-13T01:15:06Z ----------------------------------------------------------------

{attr) -> {attr}

Marius1311 commented on 2023-06-13T16:10:10Z ----------------------------------------------------------------

done.

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michalk8 commented on 2023-06-13T01:15:07Z ----------------------------------------------------------------

compute the {attr}fate probabilities <...> .

Marius1311 commented on 2023-06-13T16:11:19Z ----------------------------------------------------------------

done.

Marius1311 commented 1 year ago

makes sense. I moved it.

---

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Marius1311 commented 1 year ago

yes, I'll change this everywhere.

---

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Marius1311 commented 1 year ago

ok.

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

done.

---

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Marius1311 commented 1 year ago

I moved it to the first paragraph.

---

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Marius1311 commented 1 year ago

ok, adapted.

---

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Marius1311 commented 1 year ago

done, thanks!

---

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Marius1311 commented 1 year ago

ok.

---

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Marius1311 commented 1 year ago

well...

---

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Marius1311 commented 1 year ago

ok, done.

---

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Marius1311 commented 1 year ago

I removed these from the section heading.

---

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Marius1311 commented 1 year ago

included already (reuter:22)

---

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Marius1311 commented 1 year ago

you're right, that seems to be the case. adapted.

---

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michalk8 commented on 2023-06-13T01:10:47Z ----------------------------------------------------------------

inintial -> initial

Marius1311 commented on 2023-06-13T16:02:45Z ----------------------------------------------------------------

thanks.

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michalk8 commented on 2023-06-13T01:10:48Z ----------------------------------------------------------------

initial- -> initial

Marius1311 commented on 2023-06-13T16:03:01Z ----------------------------------------------------------------

done.

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michalk8 commented on 2023-06-13T01:10:49Z ----------------------------------------------------------------

Would not use italics for terminal.

knowlege -> knowledge

which we show below -> as shown below.

Marius1311 commented on 2023-06-13T16:03:44Z ----------------------------------------------------------------

ok.

review-notebook-app[bot] commented 1 year ago

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michalk8 commented on 2023-06-13T01:10:50Z ----------------------------------------------------------------

probabilits -> probability

Marius1311 commented on 2023-06-13T16:04:09Z ----------------------------------------------------------------

done.

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michalk8 commented on 2023-06-13T01:10:51Z ----------------------------------------------------------------

we compute the macrostates.

dashed vertical line

Marius1311 commented on 2023-06-13T16:04:49Z ----------------------------------------------------------------

ok.

review-notebook-app[bot] commented 1 year ago

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michalk8 commented on 2023-06-13T01:10:52Z ----------------------------------------------------------------

Remove the Nice!

...; however, that does -> . However, that does not

Missing . in the last sentence.

; we show below -> . We show below

" for each of the cells most confidently assigned to a certain macrostates" reads not so easily

Marius1311 commented on 2023-06-13T16:06:30Z ----------------------------------------------------------------

thanks, done

review-notebook-app[bot] commented 1 year ago

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michalk8 commented on 2023-06-13T01:10:53Z ----------------------------------------------------------------

any {attr}... -> any observation-level covariate

Link to the transport map kernel tutorial rather than the class (or both) (also missing the {class} role for the kernel).

Marius1311 commented on 2023-06-13T16:09:29Z ----------------------------------------------------------------

done.

review-notebook-app[bot] commented 1 year ago

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michalk8 commented on 2023-06-13T01:10:54Z ----------------------------------------------------------------

becasue -> because

Let's try the automatic terminal

Marius1311 commented on 2023-06-13T16:10:54Z ----------------------------------------------------------------

done.

review-notebook-app[bot] commented 1 year ago

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michalk8 commented on 2023-06-13T01:10:54Z ----------------------------------------------------------------

ductal-cell markers -> Ductal cell markers.

Marius1311 commented on 2023-06-13T16:11:44Z ----------------------------------------------------------------

done.

review-notebook-app[bot] commented 1 year ago

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michalk8 commented on 2023-06-13T01:10:55Z ----------------------------------------------------------------

as initial -> as an initial state.

Marius1311 commented on 2023-06-13T16:12:02Z ----------------------------------------------------------------

ok.

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michalk8 commented on 2023-06-13T01:10:56Z ----------------------------------------------------------------

we recommend... -> we recommend to: + go thrgouh/take a look/take a look/

Marius1311 commented on 2023-06-13T16:12:46Z ----------------------------------------------------------------

thanks!

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michalk8 commented on 2023-06-13T01:15:06Z ----------------------------------------------------------------

{attr) -> {attr}

Marius1311 commented on 2023-06-13T16:10:10Z ----------------------------------------------------------------

done.

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michalk8 commented on 2023-06-13T01:15:07Z ----------------------------------------------------------------

compute the {attr}fate probabilities <...> .

Marius1311 commented on 2023-06-13T16:11:19Z ----------------------------------------------------------------

done.

Marius1311 commented 1 year ago

makes sense. I moved it.

---

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Marius1311 commented 1 year ago

yes, I'll change this everywhere.

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

ok.

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

done.

---

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Marius1311 commented 1 year ago

I moved it to the first paragraph.

---

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Marius1311 commented 1 year ago

ok, adapted.

---

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Marius1311 commented 1 year ago

done, thanks!

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

ok.

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

well...

---

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Marius1311 commented 1 year ago

ok, done.

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

I removed these from the section heading.

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

included already (reuter:22)

---

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Marius1311 commented 1 year ago

you're right, that seems to be the case. adapted.

---

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michalk8 commented on 2023-06-13T01:10:48Z ----------------------------------------------------------------

initial- -> initial

Marius1311 commented on 2023-06-13T16:03:01Z ----------------------------------------------------------------

done.

review-notebook-app[bot] commented 1 year ago

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michalk8 commented on 2023-06-13T01:10:49Z ----------------------------------------------------------------

Would not use italics for terminal.

knowlege -> knowledge

which we show below -> as shown below.

Marius1311 commented on 2023-06-13T16:03:44Z ----------------------------------------------------------------

ok.

review-notebook-app[bot] commented 1 year ago

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michalk8 commented on 2023-06-13T01:10:50Z ----------------------------------------------------------------

probabilits -> probability

Marius1311 commented on 2023-06-13T16:04:09Z ----------------------------------------------------------------

done.

review-notebook-app[bot] commented 1 year ago

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michalk8 commented on 2023-06-13T01:10:51Z ----------------------------------------------------------------

we compute the macrostates.

dashed vertical line

Marius1311 commented on 2023-06-13T16:04:49Z ----------------------------------------------------------------

ok.

review-notebook-app[bot] commented 1 year ago

View / edit / reply to this conversation on ReviewNB

michalk8 commented on 2023-06-13T01:10:52Z ----------------------------------------------------------------

Remove the Nice!

...; however, that does -> . However, that does not

Missing . in the last sentence.

; we show below -> . We show below

" for each of the cells most confidently assigned to a certain macrostates" reads not so easily

Marius1311 commented on 2023-06-13T16:06:30Z ----------------------------------------------------------------

thanks, done

review-notebook-app[bot] commented 1 year ago

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michalk8 commented on 2023-06-13T01:10:53Z ----------------------------------------------------------------

any {attr}... -> any observation-level covariate

Link to the transport map kernel tutorial rather than the class (or both) (also missing the {class} role for the kernel).

Marius1311 commented on 2023-06-13T16:09:29Z ----------------------------------------------------------------

done.

review-notebook-app[bot] commented 1 year ago

View / edit / reply to this conversation on ReviewNB

michalk8 commented on 2023-06-13T01:10:54Z ----------------------------------------------------------------

becasue -> because

Let's try the automatic terminal

Marius1311 commented on 2023-06-13T16:10:54Z ----------------------------------------------------------------

done.

review-notebook-app[bot] commented 1 year ago

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michalk8 commented on 2023-06-13T01:10:54Z ----------------------------------------------------------------

ductal-cell markers -> Ductal cell markers.

Marius1311 commented on 2023-06-13T16:11:44Z ----------------------------------------------------------------

done.

review-notebook-app[bot] commented 1 year ago

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michalk8 commented on 2023-06-13T01:10:55Z ----------------------------------------------------------------

as initial -> as an initial state.

Marius1311 commented on 2023-06-13T16:12:02Z ----------------------------------------------------------------

ok.

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michalk8 commented on 2023-06-13T01:10:56Z ----------------------------------------------------------------

we recommend... -> we recommend to: + go thrgouh/take a look/take a look/

Marius1311 commented on 2023-06-13T16:12:46Z ----------------------------------------------------------------

thanks!

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michalk8 commented on 2023-06-13T01:15:06Z ----------------------------------------------------------------

{attr) -> {attr}

Marius1311 commented on 2023-06-13T16:10:10Z ----------------------------------------------------------------

done.

review-notebook-app[bot] commented 1 year ago

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michalk8 commented on 2023-06-13T01:15:07Z ----------------------------------------------------------------

compute the {attr}fate probabilities <...> .

Marius1311 commented on 2023-06-13T16:11:19Z ----------------------------------------------------------------

done.

Marius1311 commented 1 year ago

makes sense. I moved it.

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

yes, I'll change this everywhere.

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

ok.

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

done.

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

I moved it to the first paragraph.

---

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Marius1311 commented 1 year ago

ok, adapted.

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

done, thanks!

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

ok.

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

well...

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

ok, done.

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

I removed these from the section heading.

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

included already (reuter:22)

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

you're right, that seems to be the case. adapted.

---

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michalk8 commented on 2023-06-13T01:10:49Z ----------------------------------------------------------------

Would not use italics for terminal.

knowlege -> knowledge

which we show below -> as shown below.

Marius1311 commented on 2023-06-13T16:03:44Z ----------------------------------------------------------------

ok.

review-notebook-app[bot] commented 1 year ago

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michalk8 commented on 2023-06-13T01:10:50Z ----------------------------------------------------------------

probabilits -> probability

Marius1311 commented on 2023-06-13T16:04:09Z ----------------------------------------------------------------

done.

review-notebook-app[bot] commented 1 year ago

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michalk8 commented on 2023-06-13T01:10:51Z ----------------------------------------------------------------

we compute the macrostates.

dashed vertical line

Marius1311 commented on 2023-06-13T16:04:49Z ----------------------------------------------------------------

ok.

review-notebook-app[bot] commented 1 year ago

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michalk8 commented on 2023-06-13T01:10:52Z ----------------------------------------------------------------

Remove the Nice!

...; however, that does -> . However, that does not

Missing . in the last sentence.

; we show below -> . We show below

" for each of the cells most confidently assigned to a certain macrostates" reads not so easily

Marius1311 commented on 2023-06-13T16:06:30Z ----------------------------------------------------------------

thanks, done

review-notebook-app[bot] commented 1 year ago

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michalk8 commented on 2023-06-13T01:10:53Z ----------------------------------------------------------------

any {attr}... -> any observation-level covariate

Link to the transport map kernel tutorial rather than the class (or both) (also missing the {class} role for the kernel).

Marius1311 commented on 2023-06-13T16:09:29Z ----------------------------------------------------------------

done.

review-notebook-app[bot] commented 1 year ago

View / edit / reply to this conversation on ReviewNB

michalk8 commented on 2023-06-13T01:10:54Z ----------------------------------------------------------------

becasue -> because

Let's try the automatic terminal

Marius1311 commented on 2023-06-13T16:10:54Z ----------------------------------------------------------------

done.

review-notebook-app[bot] commented 1 year ago

View / edit / reply to this conversation on ReviewNB

michalk8 commented on 2023-06-13T01:10:54Z ----------------------------------------------------------------

ductal-cell markers -> Ductal cell markers.

Marius1311 commented on 2023-06-13T16:11:44Z ----------------------------------------------------------------

done.

review-notebook-app[bot] commented 1 year ago

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michalk8 commented on 2023-06-13T01:10:55Z ----------------------------------------------------------------

as initial -> as an initial state.

Marius1311 commented on 2023-06-13T16:12:02Z ----------------------------------------------------------------

ok.

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michalk8 commented on 2023-06-13T01:10:56Z ----------------------------------------------------------------

we recommend... -> we recommend to: + go thrgouh/take a look/take a look/

Marius1311 commented on 2023-06-13T16:12:46Z ----------------------------------------------------------------

thanks!

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michalk8 commented on 2023-06-13T01:15:06Z ----------------------------------------------------------------

{attr) -> {attr}

Marius1311 commented on 2023-06-13T16:10:10Z ----------------------------------------------------------------

done.

review-notebook-app[bot] commented 1 year ago

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michalk8 commented on 2023-06-13T01:15:07Z ----------------------------------------------------------------

compute the {attr}fate probabilities <...> .

Marius1311 commented on 2023-06-13T16:11:19Z ----------------------------------------------------------------

done.

Marius1311 commented 1 year ago

makes sense. I moved it.

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

yes, I'll change this everywhere.

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

ok.

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

done.

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

I moved it to the first paragraph.

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

ok, adapted.

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

done, thanks!

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

ok.

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

well...

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

ok, done.

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

I removed these from the section heading.

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

included already (reuter:22)

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

you're right, that seems to be the case. adapted.

---

View entire conversation on ReviewNB

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michalk8 commented on 2023-06-13T01:10:50Z ----------------------------------------------------------------

probabilits -> probability

Marius1311 commented on 2023-06-13T16:04:09Z ----------------------------------------------------------------

done.

review-notebook-app[bot] commented 1 year ago

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michalk8 commented on 2023-06-13T01:10:51Z ----------------------------------------------------------------

we compute the macrostates.

dashed vertical line

Marius1311 commented on 2023-06-13T16:04:49Z ----------------------------------------------------------------

ok.

review-notebook-app[bot] commented 1 year ago

View / edit / reply to this conversation on ReviewNB

michalk8 commented on 2023-06-13T01:10:52Z ----------------------------------------------------------------

Remove the Nice!

...; however, that does -> . However, that does not

Missing . in the last sentence.

; we show below -> . We show below

" for each of the cells most confidently assigned to a certain macrostates" reads not so easily

Marius1311 commented on 2023-06-13T16:06:30Z ----------------------------------------------------------------

thanks, done

review-notebook-app[bot] commented 1 year ago

View / edit / reply to this conversation on ReviewNB

michalk8 commented on 2023-06-13T01:10:53Z ----------------------------------------------------------------

any {attr}... -> any observation-level covariate

Link to the transport map kernel tutorial rather than the class (or both) (also missing the {class} role for the kernel).

Marius1311 commented on 2023-06-13T16:09:29Z ----------------------------------------------------------------

done.

review-notebook-app[bot] commented 1 year ago

View / edit / reply to this conversation on ReviewNB

michalk8 commented on 2023-06-13T01:10:54Z ----------------------------------------------------------------

becasue -> because

Let's try the automatic terminal

Marius1311 commented on 2023-06-13T16:10:54Z ----------------------------------------------------------------

done.

review-notebook-app[bot] commented 1 year ago

View / edit / reply to this conversation on ReviewNB

michalk8 commented on 2023-06-13T01:10:54Z ----------------------------------------------------------------

ductal-cell markers -> Ductal cell markers.

Marius1311 commented on 2023-06-13T16:11:44Z ----------------------------------------------------------------

done.

review-notebook-app[bot] commented 1 year ago

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michalk8 commented on 2023-06-13T01:10:55Z ----------------------------------------------------------------

as initial -> as an initial state.

Marius1311 commented on 2023-06-13T16:12:02Z ----------------------------------------------------------------

ok.

review-notebook-app[bot] commented 1 year ago

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michalk8 commented on 2023-06-13T01:10:56Z ----------------------------------------------------------------

we recommend... -> we recommend to: + go thrgouh/take a look/take a look/

Marius1311 commented on 2023-06-13T16:12:46Z ----------------------------------------------------------------

thanks!

review-notebook-app[bot] commented 1 year ago

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michalk8 commented on 2023-06-13T01:15:06Z ----------------------------------------------------------------

{attr) -> {attr}

Marius1311 commented on 2023-06-13T16:10:10Z ----------------------------------------------------------------

done.

review-notebook-app[bot] commented 1 year ago

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michalk8 commented on 2023-06-13T01:15:07Z ----------------------------------------------------------------

compute the {attr}fate probabilities <...> .

Marius1311 commented on 2023-06-13T16:11:19Z ----------------------------------------------------------------

done.

Marius1311 commented 1 year ago

makes sense. I moved it.

---

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Marius1311 commented 1 year ago

yes, I'll change this everywhere.

---

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Marius1311 commented 1 year ago

ok.

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

done.

---

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Marius1311 commented 1 year ago

I moved it to the first paragraph.

---

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Marius1311 commented 1 year ago

ok, adapted.

---

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Marius1311 commented 1 year ago

done, thanks!

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

ok.

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

well...

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

ok, done.

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

I removed these from the section heading.

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

included already (reuter:22)

---

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Marius1311 commented 1 year ago

you're right, that seems to be the case. adapted.

---

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michalk8 commented on 2023-06-13T01:10:51Z ----------------------------------------------------------------

we compute the macrostates.

dashed vertical line

Marius1311 commented on 2023-06-13T16:04:49Z ----------------------------------------------------------------

ok.

review-notebook-app[bot] commented 1 year ago

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michalk8 commented on 2023-06-13T01:10:52Z ----------------------------------------------------------------

Remove the Nice!

...; however, that does -> . However, that does not

Missing . in the last sentence.

; we show below -> . We show below

" for each of the cells most confidently assigned to a certain macrostates" reads not so easily

Marius1311 commented on 2023-06-13T16:06:30Z ----------------------------------------------------------------

thanks, done

review-notebook-app[bot] commented 1 year ago

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michalk8 commented on 2023-06-13T01:10:53Z ----------------------------------------------------------------

any {attr}... -> any observation-level covariate

Link to the transport map kernel tutorial rather than the class (or both) (also missing the {class} role for the kernel).

Marius1311 commented on 2023-06-13T16:09:29Z ----------------------------------------------------------------

done.

review-notebook-app[bot] commented 1 year ago

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michalk8 commented on 2023-06-13T01:10:54Z ----------------------------------------------------------------

becasue -> because

Let's try the automatic terminal

Marius1311 commented on 2023-06-13T16:10:54Z ----------------------------------------------------------------

done.

review-notebook-app[bot] commented 1 year ago

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michalk8 commented on 2023-06-13T01:10:54Z ----------------------------------------------------------------

ductal-cell markers -> Ductal cell markers.

Marius1311 commented on 2023-06-13T16:11:44Z ----------------------------------------------------------------

done.

review-notebook-app[bot] commented 1 year ago

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michalk8 commented on 2023-06-13T01:10:55Z ----------------------------------------------------------------

as initial -> as an initial state.

Marius1311 commented on 2023-06-13T16:12:02Z ----------------------------------------------------------------

ok.

review-notebook-app[bot] commented 1 year ago

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michalk8 commented on 2023-06-13T01:10:56Z ----------------------------------------------------------------

we recommend... -> we recommend to: + go thrgouh/take a look/take a look/

Marius1311 commented on 2023-06-13T16:12:46Z ----------------------------------------------------------------

thanks!

review-notebook-app[bot] commented 1 year ago

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michalk8 commented on 2023-06-13T01:15:06Z ----------------------------------------------------------------

{attr) -> {attr}

Marius1311 commented on 2023-06-13T16:10:10Z ----------------------------------------------------------------

done.

review-notebook-app[bot] commented 1 year ago

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michalk8 commented on 2023-06-13T01:15:07Z ----------------------------------------------------------------

compute the {attr}fate probabilities <...> .

Marius1311 commented on 2023-06-13T16:11:19Z ----------------------------------------------------------------

done.

Marius1311 commented 1 year ago

makes sense. I moved it.

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

yes, I'll change this everywhere.

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

ok.

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

done.

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

I moved it to the first paragraph.

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

ok, adapted.

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

done, thanks!

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

ok.

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

well...

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

ok, done.

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

I removed these from the section heading.

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

included already (reuter:22)

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

you're right, that seems to be the case. adapted.

---

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michalk8 commented on 2023-06-13T01:10:52Z ----------------------------------------------------------------

Remove the Nice!

...; however, that does -> . However, that does not

Missing . in the last sentence.

; we show below -> . We show below

" for each of the cells most confidently assigned to a certain macrostates" reads not so easily

Marius1311 commented on 2023-06-13T16:06:30Z ----------------------------------------------------------------

thanks, done

review-notebook-app[bot] commented 1 year ago

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michalk8 commented on 2023-06-13T01:10:53Z ----------------------------------------------------------------

any {attr}... -> any observation-level covariate

Link to the transport map kernel tutorial rather than the class (or both) (also missing the {class} role for the kernel).

Marius1311 commented on 2023-06-13T16:09:29Z ----------------------------------------------------------------

done.

review-notebook-app[bot] commented 1 year ago

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michalk8 commented on 2023-06-13T01:10:54Z ----------------------------------------------------------------

becasue -> because

Let's try the automatic terminal

Marius1311 commented on 2023-06-13T16:10:54Z ----------------------------------------------------------------

done.

review-notebook-app[bot] commented 1 year ago

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michalk8 commented on 2023-06-13T01:10:54Z ----------------------------------------------------------------

ductal-cell markers -> Ductal cell markers.

Marius1311 commented on 2023-06-13T16:11:44Z ----------------------------------------------------------------

done.

review-notebook-app[bot] commented 1 year ago

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michalk8 commented on 2023-06-13T01:10:55Z ----------------------------------------------------------------

as initial -> as an initial state.

Marius1311 commented on 2023-06-13T16:12:02Z ----------------------------------------------------------------

ok.

review-notebook-app[bot] commented 1 year ago

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michalk8 commented on 2023-06-13T01:10:56Z ----------------------------------------------------------------

we recommend... -> we recommend to: + go thrgouh/take a look/take a look/

Marius1311 commented on 2023-06-13T16:12:46Z ----------------------------------------------------------------

thanks!

review-notebook-app[bot] commented 1 year ago

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michalk8 commented on 2023-06-13T01:15:06Z ----------------------------------------------------------------

{attr) -> {attr}

Marius1311 commented on 2023-06-13T16:10:10Z ----------------------------------------------------------------

done.

review-notebook-app[bot] commented 1 year ago

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michalk8 commented on 2023-06-13T01:15:07Z ----------------------------------------------------------------

compute the {attr}fate probabilities <...> .

Marius1311 commented on 2023-06-13T16:11:19Z ----------------------------------------------------------------

done.

Marius1311 commented 1 year ago

makes sense. I moved it.

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

yes, I'll change this everywhere.

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

ok.

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

done.

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

I moved it to the first paragraph.

---

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Marius1311 commented 1 year ago

ok, adapted.

---

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Marius1311 commented 1 year ago

done, thanks!

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

ok.

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

well...

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

ok, done.

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

I removed these from the section heading.

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

included already (reuter:22)

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

you're right, that seems to be the case. adapted.

---

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michalk8 commented on 2023-06-13T01:10:53Z ----------------------------------------------------------------

any {attr}... -> any observation-level covariate

Link to the transport map kernel tutorial rather than the class (or both) (also missing the {class} role for the kernel).

Marius1311 commented on 2023-06-13T16:09:29Z ----------------------------------------------------------------

done.

review-notebook-app[bot] commented 1 year ago

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michalk8 commented on 2023-06-13T01:10:54Z ----------------------------------------------------------------

becasue -> because

Let's try the automatic terminal

Marius1311 commented on 2023-06-13T16:10:54Z ----------------------------------------------------------------

done.

review-notebook-app[bot] commented 1 year ago

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michalk8 commented on 2023-06-13T01:10:54Z ----------------------------------------------------------------

ductal-cell markers -> Ductal cell markers.

Marius1311 commented on 2023-06-13T16:11:44Z ----------------------------------------------------------------

done.

review-notebook-app[bot] commented 1 year ago

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michalk8 commented on 2023-06-13T01:10:55Z ----------------------------------------------------------------

as initial -> as an initial state.

Marius1311 commented on 2023-06-13T16:12:02Z ----------------------------------------------------------------

ok.

review-notebook-app[bot] commented 1 year ago

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michalk8 commented on 2023-06-13T01:10:56Z ----------------------------------------------------------------

we recommend... -> we recommend to: + go thrgouh/take a look/take a look/

Marius1311 commented on 2023-06-13T16:12:46Z ----------------------------------------------------------------

thanks!

review-notebook-app[bot] commented 1 year ago

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michalk8 commented on 2023-06-13T01:15:06Z ----------------------------------------------------------------

{attr) -> {attr}

Marius1311 commented on 2023-06-13T16:10:10Z ----------------------------------------------------------------

done.

review-notebook-app[bot] commented 1 year ago

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michalk8 commented on 2023-06-13T01:15:07Z ----------------------------------------------------------------

compute the {attr}fate probabilities <...> .

Marius1311 commented on 2023-06-13T16:11:19Z ----------------------------------------------------------------

done.

Marius1311 commented 1 year ago

makes sense. I moved it.

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

yes, I'll change this everywhere.

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

ok.

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

done.

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

I moved it to the first paragraph.

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

ok, adapted.

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

done, thanks!

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

ok.

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

well...

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

ok, done.

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

I removed these from the section heading.

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

included already (reuter:22)

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

you're right, that seems to be the case. adapted.

---

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michalk8 commented on 2023-06-13T01:10:54Z ----------------------------------------------------------------

becasue -> because

Let's try the automatic terminal

Marius1311 commented on 2023-06-13T16:10:54Z ----------------------------------------------------------------

done.

review-notebook-app[bot] commented 1 year ago

View / edit / reply to this conversation on ReviewNB

michalk8 commented on 2023-06-13T01:10:54Z ----------------------------------------------------------------

ductal-cell markers -> Ductal cell markers.

Marius1311 commented on 2023-06-13T16:11:44Z ----------------------------------------------------------------

done.

review-notebook-app[bot] commented 1 year ago

View / edit / reply to this conversation on ReviewNB

michalk8 commented on 2023-06-13T01:10:55Z ----------------------------------------------------------------

as initial -> as an initial state.

Marius1311 commented on 2023-06-13T16:12:02Z ----------------------------------------------------------------

ok.

review-notebook-app[bot] commented 1 year ago

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michalk8 commented on 2023-06-13T01:10:56Z ----------------------------------------------------------------

we recommend... -> we recommend to: + go thrgouh/take a look/take a look/

Marius1311 commented on 2023-06-13T16:12:46Z ----------------------------------------------------------------

thanks!

review-notebook-app[bot] commented 1 year ago

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michalk8 commented on 2023-06-13T01:15:06Z ----------------------------------------------------------------

{attr) -> {attr}

Marius1311 commented on 2023-06-13T16:10:10Z ----------------------------------------------------------------

done.

review-notebook-app[bot] commented 1 year ago

View / edit / reply to this conversation on ReviewNB

michalk8 commented on 2023-06-13T01:15:07Z ----------------------------------------------------------------

compute the {attr}fate probabilities <...> .

Marius1311 commented on 2023-06-13T16:11:19Z ----------------------------------------------------------------

done.

Marius1311 commented 1 year ago

makes sense. I moved it.

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

yes, I'll change this everywhere.

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

ok.

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

done.

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

I moved it to the first paragraph.

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

ok, adapted.

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

done, thanks!

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

ok.

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

well...

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

ok, done.

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

I removed these from the section heading.

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

included already (reuter:22)

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

you're right, that seems to be the case. adapted.

---

View entire conversation on ReviewNB

Next

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michalk8 commented on 2023-06-13T01:10:54Z ----------------------------------------------------------------

ductal-cell markers -> Ductal cell markers.

Marius1311 commented on 2023-06-13T16:11:44Z ----------------------------------------------------------------

done.

review-notebook-app[bot] commented 1 year ago

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michalk8 commented on 2023-06-13T01:10:55Z ----------------------------------------------------------------

as initial -> as an initial state.

Marius1311 commented on 2023-06-13T16:12:02Z ----------------------------------------------------------------

ok.

review-notebook-app[bot] commented 1 year ago

View / edit / reply to this conversation on ReviewNB

michalk8 commented on 2023-06-13T01:10:56Z ----------------------------------------------------------------

we recommend... -> we recommend to: + go thrgouh/take a look/take a look/

Marius1311 commented on 2023-06-13T16:12:46Z ----------------------------------------------------------------

thanks!

review-notebook-app[bot] commented 1 year ago

View / edit / reply to this conversation on ReviewNB

michalk8 commented on 2023-06-13T01:15:06Z ----------------------------------------------------------------

{attr) -> {attr}

Marius1311 commented on 2023-06-13T16:10:10Z ----------------------------------------------------------------

done.

review-notebook-app[bot] commented 1 year ago

View / edit / reply to this conversation on ReviewNB

michalk8 commented on 2023-06-13T01:15:07Z ----------------------------------------------------------------

compute the {attr}fate probabilities <...> .

Marius1311 commented on 2023-06-13T16:11:19Z ----------------------------------------------------------------

done.

Marius1311 commented 1 year ago

makes sense. I moved it.

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

yes, I'll change this everywhere.

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

ok.

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

done.

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

I moved it to the first paragraph.

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

ok, adapted.

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

done, thanks!

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

ok.

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

well...

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

ok, done.

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

I removed these from the section heading.

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

included already (reuter:22)

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

you're right, that seems to be the case. adapted.

---

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michalk8 commented on 2023-06-13T01:10:55Z ----------------------------------------------------------------

as initial -> as an initial state.

Marius1311 commented on 2023-06-13T16:12:02Z ----------------------------------------------------------------

ok.

review-notebook-app[bot] commented 1 year ago

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michalk8 commented on 2023-06-13T01:10:56Z ----------------------------------------------------------------

we recommend... -> we recommend to: + go thrgouh/take a look/take a look/

Marius1311 commented on 2023-06-13T16:12:46Z ----------------------------------------------------------------

thanks!

review-notebook-app[bot] commented 1 year ago

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michalk8 commented on 2023-06-13T01:15:06Z ----------------------------------------------------------------

{attr) -> {attr}

Marius1311 commented on 2023-06-13T16:10:10Z ----------------------------------------------------------------

done.

review-notebook-app[bot] commented 1 year ago

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michalk8 commented on 2023-06-13T01:15:07Z ----------------------------------------------------------------

compute the {attr}fate probabilities <...> .

Marius1311 commented on 2023-06-13T16:11:19Z ----------------------------------------------------------------

done.

Marius1311 commented 1 year ago

makes sense. I moved it.

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

yes, I'll change this everywhere.

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

ok.

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

done.

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

I moved it to the first paragraph.

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

ok, adapted.

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

done, thanks!

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

ok.

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

well...

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

ok, done.

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

I removed these from the section heading.

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

included already (reuter:22)

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

you're right, that seems to be the case. adapted.

---

View entire conversation on ReviewNB

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michalk8 commented on 2023-06-13T01:10:56Z ----------------------------------------------------------------

we recommend... -> we recommend to: + go thrgouh/take a look/take a look/

Marius1311 commented on 2023-06-13T16:12:46Z ----------------------------------------------------------------

thanks!

review-notebook-app[bot] commented 1 year ago

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michalk8 commented on 2023-06-13T01:15:06Z ----------------------------------------------------------------

{attr) -> {attr}

Marius1311 commented on 2023-06-13T16:10:10Z ----------------------------------------------------------------

done.

review-notebook-app[bot] commented 1 year ago

View / edit / reply to this conversation on ReviewNB

michalk8 commented on 2023-06-13T01:15:07Z ----------------------------------------------------------------

compute the {attr}fate probabilities <...> .

Marius1311 commented on 2023-06-13T16:11:19Z ----------------------------------------------------------------

done.

Marius1311 commented 1 year ago

makes sense. I moved it.

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

yes, I'll change this everywhere.

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

ok.

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

done.

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

I moved it to the first paragraph.

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

ok, adapted.

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

done, thanks!

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

ok.

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

well...

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

ok, done.

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

I removed these from the section heading.

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

included already (reuter:22)

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

you're right, that seems to be the case. adapted.

---

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michalk8 commented on 2023-06-13T01:15:06Z ----------------------------------------------------------------

{attr) -> {attr}

Marius1311 commented on 2023-06-13T16:10:10Z ----------------------------------------------------------------

done.

review-notebook-app[bot] commented 1 year ago

View / edit / reply to this conversation on ReviewNB

michalk8 commented on 2023-06-13T01:15:07Z ----------------------------------------------------------------

compute the {attr}fate probabilities <...> .

Marius1311 commented on 2023-06-13T16:11:19Z ----------------------------------------------------------------

done.

Marius1311 commented 1 year ago

makes sense. I moved it.

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

yes, I'll change this everywhere.

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

ok.

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

done.

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

I moved it to the first paragraph.

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

ok, adapted.

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

done, thanks!

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

ok.

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

well...

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

ok, done.

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

I removed these from the section heading.

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

included already (reuter:22)

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

you're right, that seems to be the case. adapted.

---

View entire conversation on ReviewNB

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michalk8 commented on 2023-06-13T01:15:07Z ----------------------------------------------------------------

compute the {attr}fate probabilities <...> .

Marius1311 commented on 2023-06-13T16:11:19Z ----------------------------------------------------------------

done.

Marius1311 commented 1 year ago

makes sense. I moved it.

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

yes, I'll change this everywhere.

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

ok.

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

done.

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

I moved it to the first paragraph.

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

ok, adapted.

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

done, thanks!

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

ok.

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

well...

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

ok, done.

---

View entire conversation on ReviewNB

Marius1311 commented 1 year ago

I removed these from the section heading.

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Marius1311 commented 1 year ago

included already (reuter:22)

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Marius1311 commented 1 year ago

you're right, that seems to be the case. adapted.

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Next

• © Githubissues.
• Githubissues is a development platform for aggregating issues.

[Marius1311]

makes sense. I moved it.

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[Marius1311]

yes, I'll change this everywhere.

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[Marius1311]

ok.

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[Marius1311]

done.

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[Marius1311]

I moved it to the first paragraph.

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[Marius1311]

ok, adapted.

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[Marius1311]

done, thanks!

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[Marius1311]

ok.

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[Marius1311]

well...

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[Marius1311]

ok, done.

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[Marius1311]

I removed these from the section heading.

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[Marius1311]

included already (reuter:22)

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[Marius1311]

you're right, that seems to be the case. adapted.

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