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Dr. Fan,
Maybe this is irrelevant to irGSEA, probably more related to the Heatmap package but is there anyway that I can keep the pathway order? It seems like even if I use cluster_row=FALSE param…
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When running inside a git clone which is using SSH git location.
mitar updated
5 months ago
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Hi,
When classifying some Refseq sequences I noticed that some plasmids are being classified as virus. For example the reference assembly of Klebsiella pneumoniae (https://www.ncbi.nlm.nih.gov/data…
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Hi, I am trying to run the gsva on a seurat object with an assembled database form multiple origins. I already tested it with a subset of the seurat object and the subset of the database.
For inst…
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Dear Guangchuang,
Big fan of all the R suites your group develop!
I have a question regarding the universal gene list used in the `enricher` function for the Over Representation Analysis.
Test …
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Hi team,
After run gsva, I have pathway score. Then I try to find association between pathways of interested using cor.test(). However, when I pick two random pathways to find their association, it…
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Hello,
I was using decoupleR for pathway analysis in single cell.
I tried a few lines:
```R
msigdb
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HI Chuiqin,
I met a problem like below when I run your tutorial, could you help me debug this issue? Thanks a ton!
> irGSEA.density.scatterplot(object = pbmc3k.final, method = "UCell", show.geneset …
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Hi YuLab members,
Are there any ways to run enrichGO() function on MSigDB gene set (like HALLMARK gene set)?
Best,
Keren
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Hello,
I've the following AMR format, but it raises a warning and error:
```
# ::tok Hallmark could make a fortune off of this guy .
# ::alignments 0-1.1.1.2.1 1-1 2-1.1 4-1.1.2 6-1.1.2.1.r 7-…