fgsea

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Question: Visium Data and pulling out cells with high GO enrichment for a given pathway

8

Hi, I am using your package on Visium data as described in your recent manual, it works very fine! Related to that, I am wondering if there is a way...

DirtyHarry80

Unbalanced gene-level statistic warning

1

Hello! Thank you for the development and maintenance of this project! When using `fgsea` function I got a warning: ``` In fgseaMultilevel(...) : There were 1 pathways for which P-values...

TatiKarp

Questions with the scoreType = 'pos'

1

Hello there! First of all, thanks for implementing the pre-ranked gsea algorithm in R, which is really helpful. I'm using the package for my current project and there are several...

noblegasss

Use outside of R

4

Hi, everyone in @ctlab. This is @maxkfranz from @cytoscape (U. Toronto). I hope this message finds you well. FGSEA is a great algorithm, and it would be useful to have...

maxkfranz

Questions related to fgsea algorithm

1

Hi there! Thanks a lot for your package, it's really a great tool. I have been using it for many years, but I recently came across some methodological discussion in...

lucolotto

Citation

3

Hi, is there a peer reviewed publication for fgsea? I saw the preprint but would love to be able to cite the published work in some papers of ours. Thanks!

pstew

collapsePathways() errors in padj threshold-dependent fashion after successful fgsea() run

7

Hello, First of all, thanks for writing/maintaining such a fantastic package! I have recently encountered an issue with the collapsePathways() function in fgsea 1.6.0, in which I get the following...

ajw2329

direction of pathway change in the results

2

Hi, Thanks so much for developing this package. I'm struggling to understand the direction of change for the significant pathways in the results. According to the Broad GSEA [website,](https://www.gsea-msigdb.org/gsea/doc/GSEAUserGuideTEXT.htm) ES...

zhangguy

fgsea hangs with nperm=1001, but not 1000

6

``` # Runs fine, takes just a few seconds fgseaRes

assaron

scRNA-seq: how to create the Ranked list?

19

Hello, I have some clusters with differentially expresses genes generated using Seurat. I also have a highly curated gene list and I wish to perform enrichment analysis using these on...

asmariyaz23