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theislab / cellrank_notebooks

Tutorials and examples for CellRank.
https://cellrank.org
BSD 3-Clause "New" or "Revised" License
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Feature/pseudotime tutorial #48

Closed Marius1311 closed 2 years ago

Marius1311 commented 2 years ago

This adds a tutorial for the pseudotime kernel using the bone marrow data. I'll have to upload this to Figshare and include in cellrank.datasets, see https://github.com/theislab/cellrank/issues/884

closes #47

review-notebook-app[bot] commented 2 years ago

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review-notebook-app[bot] commented 2 years ago

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michalk8 commented on 2022-06-14T14:02:42Z ----------------------------------------------------------------

Would drop ... and use :

We can summarize -> we summarize


Marius1311 commented on 2022-06-14T16:21:22Z ----------------------------------------------------------------

I disagree with the former and agree with the latter.

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michalk8 commented on 2022-06-14T14:02:43Z ----------------------------------------------------------------

Fix typos + use kNN instead of KNN


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michalk8 commented on 2022-06-14T14:02:44Z ----------------------------------------------------------------

I feel like this whole sentence is redundant, would remove.


Marius1311 commented on 2022-06-14T16:23:17Z ----------------------------------------------------------------

ok.

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michalk8 commented on 2022-06-14T14:02:44Z ----------------------------------------------------------------

The we're exploring in this tutorial reads weird, would remove or reformulate.

Also would add citation to scVelo




Marius1311 commented on 2022-06-14T16:24:52Z ----------------------------------------------------------------

ok.

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michalk8 commented on 2022-06-14T14:02:46Z ----------------------------------------------------------------

Maybe explain (very briefly) why this looks fine/expected?


Marius1311 commented on 2022-06-14T16:26:05Z ----------------------------------------------------------------

ok

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michalk8 commented on 2022-06-14T14:02:46Z ----------------------------------------------------------------

Remove the info about the MacBook, this will be run on the CI anyways.


Marius1311 commented on 2022-06-14T16:26:40Z ----------------------------------------------------------------

No; for a user who runs this on their computer, it's a good pointer to know roughly how long it takes to execute this on their own machine.

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michalk8 commented on 2022-06-14T14:02:47Z ----------------------------------------------------------------

The alt parameter in <img> seems wrong.


Marius1311 commented on 2022-06-14T16:27:32Z ----------------------------------------------------------------

Thanks for spotting this.

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michalk8 commented on 2022-06-14T14:02:48Z ----------------------------------------------------------------

There are a lot


Marius1311 commented on 2022-06-14T16:27:55Z ----------------------------------------------------------------

ok.

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michalk8 commented on 2022-06-14T14:02:49Z ----------------------------------------------------------------

Capitalize Palantir


Marius1311 commented on 2022-06-14T16:28:35Z ----------------------------------------------------------------

ok.

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michalk8 commented on 2022-06-14T14:02:49Z ----------------------------------------------------------------

Once I refactor str to behave as repr, the print will not be necessary


Marius1311 commented on 2022-06-14T16:28:47Z ----------------------------------------------------------------

ok.

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michalk8 commented on 2022-06-14T14:02:50Z ----------------------------------------------------------------

Would say We can again visualize ...

KNN -> kNN


Marius1311 commented on 2022-06-14T16:29:30Z ----------------------------------------------------------------

ok.

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michalk8 commented on 2022-06-14T14:02:51Z ----------------------------------------------------------------

Change high-dimensions to high dimensional data.


Marius1311 commented on 2022-06-14T16:30:27Z ----------------------------------------------------------------

ok.

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michalk8 commented on 2022-06-14T14:02:52Z ----------------------------------------------------------------

Would prefer not to use ... but : instea

Extra space in the end for best for your data .


Marius1311 commented on 2022-06-14T16:31:04Z ----------------------------------------------------------------

Citation will be inserted there, should see it once we render this.

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michalk8 commented on 2022-06-14T14:02:53Z ----------------------------------------------------------------

Would remove this line.


Marius1311 commented 2 years ago

I disagree with the former and agree with the latter.

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Marius1311 commented 2 years ago

ok.

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Marius1311 commented 2 years ago

ok.

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Marius1311 commented 2 years ago

ok

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Marius1311 commented 2 years ago

No; for a user who runs this on their computer, it's a good pointer to know roughly how long it takes to execute this on their own machine.

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Marius1311 commented 2 years ago

Thanks for spotting this.

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Marius1311 commented 2 years ago

ok.

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Marius1311 commented 2 years ago

ok.

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Marius1311 commented 2 years ago

ok.

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Marius1311 commented 2 years ago

ok.

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Marius1311 commented 2 years ago

ok.

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Marius1311 commented 2 years ago

Citation will be inserted there, should see it once we render this.

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Marius1311 commented 2 years ago

Thanks for your feedback @michalk8, I incorporated your suggested changes.

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