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Would it be possible to implement a function that can plot (for a given gene set) a GSEA plot similar to the one here:
[https://yulab-smu.top/biomedical-knowledge-mining-book/enrichplot.html#runnin…
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Hello, how to rank genes for GSEA? I have disease fibroblasts and control fibroblasts and I ran findmarkers() on them.
is the avg_log2fc sufficient to rank the genes for GSEA using clusterprofiler…
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Hello,
I'm looking for the C5 Ontology gene sets https://www.gsea-msigdb.org/gsea/msigdb/human/genesets.jsp?collection=C5 but cannot find them in your Genesets_data
![image](https://github.com/user…
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Warning in RunGSEA(srt = scData.OST.l[[i]], group_by = paste0("Standardpca_SNN_res.", :
All values in the geneScore are greater than zero. Set scoreType = 'pos'.
Species: Homo_sapiens
Loading ca…
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### Describe your issue
I run GSEA() for a goat RNAseq differention analysis results.
the prepare code is follow:
```
genelogFC
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use scale_size_area instead of scale radius. can set a ceiling that way
```
scale_size_area(#name="NOM p-val",
# limits=c(0.1,0.00001),
# range=range,
…
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Hello, when running 'imt_gsea', I encountered an error: 'TypeError: gsea() got an unexpected keyword argument 'perm_index'.' I've tried various methods but still can't resolve it. Can you help me? The…
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Currently the format of the file to be uploaded is not explicitly documented, even at the code (software docs) level. Ideally, we would have more explanation both in the code and directly on the web i…
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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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When using https://discovery.indra.bio/gene/discrete
- Often get timeout (504 error) with the default gene list, if including INDRA path-based analysis
- The result lists cannot be downloaded in any…