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When using `run_pathfindR`, is it possible to identify whether the gene set/pathway term is globally up or down regulated, i.e activated or repressed in the group of interest? I've performed pathway a…
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https://mp.weixin.qq.com/s/1v3w4ReX-fevQmw_sZVjIQ
ixxmu updated
2 years ago
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Thanks for this great package!
I have a question regarding the comparison of genesets within a cell. I want to use the C8 collection and determine which of those gene sets is the most enriched in a…
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Hello,
I am running the vignette on the 10XMultiome dataset, and hitting an error that I'm unsure how to resolve.
```
pbmc
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Hi @timoast
This is in continuation with #744. After following the merging vignette, DA is not capturing the biology and perhaps the LogFC using `FindMarkers`, all region showed in the same directi…
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specifically, the MSigDB Hallmark 2020 Geneset converted to murine orthologs
http://bioinf.wehi.edu.au/software/MSigDB/
publicly available online?
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https://github.com/mcanouil/analysis_templates/blob/67dce67de0a67f46261ad323209868894822285f/R/12-ora_gsea.R#L342-L347
```
write_xlsx(
x = setNames(lapply(enrich_sets, FUN = function(.enrich) {…
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Hello!
From https://github.com/satijalab/seurat/issues/3521 I learned how to plot a list of genes onto one dot plot:
```
nklist
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Hi!
i was wondering, if i include two different ranking databases during the pySCENIC ctx step, which have either 10kb UP and down of TSS or 500bp up and 100 down annotations, then does pySCENIC in…
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When I run `devtools::document()`, I found many messages not useful to me, they would not generate NOTEs in check because most of the functions share same arguments or are documented in the same file.…