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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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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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Hi,
I am working with compareCluster, trying to do a GSEA analysis using homemade annotation. To do so I decide to use Universal enrichment analysis.
I have a TERM2GENE and TERM2NAME. I am tryin…
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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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I run imt_gsea in linux command line:
~$ imt_gsea -i ~/cyf/IMAGEGENE/Imt_cth_z_reflect_pls/pls_analysis.pkl -g Allen_Brain_Atlas_up -o ~/cyf/IMAGEGENE/AHBA
2024-06-06 18:07:16,803: Performing GSE…
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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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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…
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**Project description**
Gene Set Enrichment Analysis (GSEA) is a computational method that determines whether an a priori defined set of genes shows statistically
significant, concordant differences…
idlip updated
2 months ago
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Hi,
Now, enriched terms are either up- or down regulated, likely because of the weighting in the running sum implementation. However, there must be terms with mixed enrichment, where some type of m…