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Hi! I have been trying to use DecipherSeq for analyzing my NMF results. However, I have encountered difficulties in annotating the themes of the modules. My modules seem to encompass a wide range …
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It would be great to have an automatic record of the settings used for Gene Set Enrichment and the ability to save the results table in the vistory.
Also, I haven't found a description for the Gira…
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Hello,
I am using the function compareCluster for three different lists of genes (Drosophila melanogaster; flybase Fbgn). When I have the results I observe that not all the genes are used for the e…
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Dear authors, I am now using ssgsea method in gsva to evaluate the samples' enrichment score in a dataset, but the result is all NA, I would be very grateful if you could give me some guidance on that…
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Hi!
In performing gene set enrichment analysis on DSS output, how do I generate a background set? I tried setting the p.threshold in callDMR to 1.0 but I'm not sure if this is the right approach.
…
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Hello,
I am running fgsea on my custom_pathways. I have 445 pathways with rather large gene-sets (see the histogram plot).
![custom_pathways_distribution](https://github.com/ctlab/fgsea/assets/67…
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Hi,
Hoping I'm not missing something obvious. I've been persistently getting an error when running analyseWGCNA(), and happens every time I run it. I've tried both with my data, and with example data…
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Hello!
I've finished analyzing a large cohort using 0/1 numerical values for control/case status respectively.
Then I went to my vcf to count the distributions of variants for each group.
But wh…
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Initial outline given by Rani attached.
[GSEA-gEAR.docx](https://github.com/IGS/gEAR/files/8343067/GSEA-gEAR.docx)
[DiffxPy](
https://diffxpy.readthedocs.io/en/latest/api/index.html#gene-set-enri…
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Dear nicheNetR Team,
Following my nichnetr analysis, I have generated a list of target genes and I am interested in assigning pathways to these genes. Could you kindly advise if there is a function…