search

YuLab-SMU / clusterProfiler

:bar_chart: A universal enrichment tool for interpreting omics data
https://yulab-smu.top/biomedical-knowledge-mining-book/
967 stars 246 forks source link

feature request: add message suggesting to cite fgsea package when it's used for GSEA analysis #680

Closed assaron closed 2 months ago

assaron commented 3 months ago

Hi, I believe some of your package users don't realize that they rely on fgsea package when they do GSEA analysis with clusterProfiler and consequently don't cite it. Could you please add a message suggesting users to cite fgsea when it's ran? For example, this is done in DESeq2 when a dedicated external method is used for logFC shrinkage: https://github.com/thelovelab/DESeq2/blob/devel/R/lfcShrink.R#L349

guidohooiveld commented 3 months ago

Sounds like a very reasonable request to me!

Actively pinging Guangchuang (@GuangchuangYu) since I expect he isn't checking the clusterProfiler GitHub every day.

GuangchuangYu commented 2 months ago

see https://github.com/YuLab-SMU/DOSE/commit/320aba3dcb40b765412a3fcb6ad2b0cc0faffecf.

assaron commented 2 months ago

Great, thanks!