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Hi, I am using Monocle to look at differential gene expression across a pseudotime trajectory. I have successfully ordered my cells and I am now trying to use plot_genes_in_pseudotime as well as plot_…
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Hi,Thanks for your great tools of monocle,.
When I used it with plot_genes_branched_pseudotime, I got the resulte of figure as follows, but I could not understand it, I do not know what was meaning…
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Hi,
I am trying to plot my XDE results with the plotXDEHm function, but I get this error:
```Error: Length of `breaks` should be equal to `colors`.```
Debugging brought me to line 142 in plotXD…
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Hello,
I performed trajectory analysis on a dataset containing human monocytes and its progenitor cells. When I tried to plot genes that changed expression over pseudotime I get a plot that looks l…
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Hello,
I have successfully used my Seurat objects with Monocle3 to get a trajectory plot. Now, I want to plot individual genes in pseudotime as in the example here https://cole-trapnell-lab.github.…
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Dear Hector,
First of all, I would like to congratulate you for your package and for your paper, it is an amazing work. I would like to open a discussion with you about how to interpret some results…
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Hi,
I've trying to work on this for days and hope ppl here can provide me some solution. Currently, I set 6 knots and I have 7 lineages.
My codes are:
`Slingshot
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Hi, Dongyuan! I have a question about generating scRNA-seq data using gaussian family.
When I generate scRNA-seq data with gaussian family like the code below
```
example_data
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Dear all,
I'd like to find upregulated / downregulated genes over trajectory.
Is there any way to make a graph of plot_genes_in_pseudotime() for Module? I want to know how each modules changes ove…
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Dear CAPITAL developers,
I am reaching again regarding the issue of plotting any sort of gene expression trends in custom dataset. When I run the tutorial and example data, everything works (except…