Alexey Sergushichev
Alexey Sergushichev
@Pedramto89 the images look OK on the first glance. What exactly are you missing?
@guidohooiveld thanks for the report. I can reproduce the problem. I'll check later what's going on.
To keep you updated: this is turned out to be an issue of the algorithm we were generally aware of, although not in this setting. Anyway we recently developed an...
Potential fix could be setting canvas for webgl to have higher pixel sizes combined with zoom, e.g 50%
Sorry for not replying you earlier. Yes, it seems that appending columns got broken at some point. I'm not sure we'll be able to fix that soon.
@shashj we also consider implementing limma+voom based pipeline, as there visualization and differential expression are coupled better, compared to DESeq2, where `rlog` transformation is better for visualization, and raw counts...
On the second glance, implementing the geometric mean normalization isn't that hard, the DESeq2 implementation is pretty straightforward: https://github.com/mikelove/DESeq2/blob/master/R/core.R#L481
Hi, 1. Not, `scoreType="pos"` doesn't require for the input stats vector to be positive. 2. Classic pre-ranked GSEA is a two-tailed test: both positive and negative enrichment are of interest....
Hi, The core of FGSEA is written in C++ so I don't see any critical obstacles for it to be used independent of R environment. It's not trivial but pretty...
I think these are the main points, that have to be addressed: 1) What's the best (or at least suitable) way to maintain two interfaces, e.g. with R and Python:...