Greg Sepich-Poore

Hello, Thanks so much for making this package. For my workflow, I am analyzing abundance data in R and then exporting it to Qiime 2 for other analyses (e.g., Songbird)....

How to cite Mfannot?

1

Hello, I'd like to cite Mfannot as a tool in a paper but am unsure exactly what to reference besides this Github repo. Is there a particular paper you'd recommend...

Batch correction concerns and questions

3

Hi @gtonkinhill, thanks for the really detailed analyses. This looks like it took a lot of time to put together, and I genuinely appreciate the public release on Github. I...

Permutation test yields significant p-values for random gene sets when using a weighted score

3

**Package:** nicolerg/ssGSEA2 (The R package implementation endorsed by the [Broad Institute's ssGSEA2.0 page](https://github.com/broadinstitute/ssGSEA2.0)) **CC:** @nicolerg **Problem Description** When running `ssGSEA2::run_ssGSEA2()` with the recommended parameters for a weighted analysis (`weight =...