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When we resolve #32, we will need a section in the manual showing the user clicking on a path to retrieve a subset of cells, then passing them to plot_genes_in_pseudotime to look at dynamics of specif…
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Hello,
I was wondering if you were planning on adding an option to merge lineages?
I'm using monocle3 and there are a lot of spurious lineages with end points that should be merged.
If you perhap…
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** If this is a question and not a bug report or enhancement request, please post to our google group at https://groups.google.com/forum/#!forum/monocle-3-users**
**Describe the bug**
I'm trying t…
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Hello!
When I am trying to run "predictSmooth" function (either for my data or as in example provided: https://statomics.github.io/tradeSeq/reference/predictSmooth.html) I got an error: **could not…
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Hi,
I am trying to use plot_pseudotime_heatmap to map the heatmap of our source, but it doesn`t work in monocle. And there are no error and result. Someone said may be I need a raw data to as the cd…
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Hi, it seems the conditions vignette does not have any code on those plots:
https://bioconductor.org/packages/release/bioc/vignettes/slingshot/inst/doc/conditionsVignette.html
especially the…
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Dear Kelly,
Many thanks for developping Slingshot - It fits perfectly my needs in term of TI. I have one small issue regarding visualization.. and I'm pretty sure you could have some ideas how to s…
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Upon running
```
from cellrank.tools.kernels import PalantirKernel
pk = PalantirKernel(adata, time_key='dpt_pseudotime').compute_transition_matrix()
print(pk)
from cellrank.tools import GPCCA
g …
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Given a single cell data for a specific cell type A from both disease and healthy population. I was wondering would it be possible to do the pseudo time trajectory analysis for only cell type A?
This…
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Hi there,
I'm running the code for bulk RNA seq time course data. But my gamList is not a large list composed by each gene. So I cannot not proceed to look at fit for each gene.
## fit GAM
gamL…