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Paper: https://www.nature.com/articles/nmeth.3971
R package: https://bioconductor.org/packages/release/bioc/html/destiny.html
@dsouz072 Please add this to current EnsembleMerge package (set up a p…
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* Pseudotime for cycles doesn't make any sense, because the non-directed geodesic distances are used
* `calculate_pseudotime` shouldn't just root the trajectory as it sees fit. The rooting should…
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I'm working on this and would like to incorporate some feedback about decision-making from one of the end-of-course surveys. Here's what it said:
_I think it would be incredibly useful if you could…
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The tutorial section entitled "Finding genes that change as a function of pseudotime" helps to find which genes change using pseudotime, but all over the graph. When I tried this approach I received …
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Hi,
I have been getting this error: ZeroDivisionError: float division by zero
when trying to run the following code:
``
de.test.wald(
data=adata_human,
gene_names=adata_human.var_name…
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Hi,
Is there a way to plot a specific cell_metadata column (e.g. a cell score for a specific process) along the pseudotime, in a similar fashion to the [plot_genes_in_pseudotime](https://rdrr.io/bi…
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I'm trying to change the default heatmap coloring scheme of monocle 3's plot_pseudotime_heatmap to that of Monocle 2's coloring scheme (see image). Does anyone know the default coloring scheme code th…
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We have a single cell time series data set (same cell type) that we're trying to get pseudotime for. We want it to have a single trajectory with no branching since the only variable factor is time. Is…
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When passing arguments into run_Slingshot.py, the outPrefix argument seems to only take the first letter of the argument and discard the rest.
When this is run:
```
python scripts/runSlingshot.py -…
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Hi Monocle Developers !!
I am facing this error when using plot_genes_in_pseudotime.
Error in attributes(out)