hypeR
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montilab
An R Package for Geneset Enrichment Workflows
Hi Monti Lab team, Thanks for assembling this great toolkit! It's really streamlining my DEG pathway analysis. I've run into a bug around retrieving the MSigDB C7 (Immunologic Signatures) gene...
I realized that `.kstest`, as it is now implemented, does not match `ks.test`'s behavior when `alternative != "two.sided"`. In particular, the score in `ks.test` is defined as follows: STATISTIC
`rctbl_build` doesn't work at present when running ks test. It would be ideal to fix it and have it report, instead of the 'hits' (not relevant), the features in the...
It would be worthwhile to implement a version of the score similar to the one implemented in GSVA, where the difference between the top positive peak and the top negative...
Ideally, when hypeR is called with the KS test, the hypeR-dot plot should color-code the dots based on whether a geneset is positively (red) or negatively (blue) skewed (w/ white...
The data table returned by hypeR includes in the hits column the names of the features (genes) separated by commas. To make it more robust, these names should be quoted,...
When assigning a rgsets object to a new variable, this variable is only a reference to the old object, not a new one. Here is an example: ``` # genesets...