multiGSEA
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lianos
NOTE: This package has been renamed to sparrow and will be submitted to Bioconductor 3.14. Please use that package instead. This is kept here for posterity.
https://github.com/lianos/multiGSEA/blob/19006d1053db8de807b80faa2a967a49d0b2ab38/R/get-reactome.R#L15 It looks like the `id.col` is not used, e.g. specifying `ensembl` as the desired featureType doesn't have an effect?
When we're playing with single cell data, some methods get tripped up when the expression-like matrix is a sparse `Matrix`, ie. a `dgCMatrix`. We need to fix this. One option...
Given a GSEA result, users can be left to wonder which genes are "pushing" the GSEA result one way or the other. Currently there is an interactive method to explore...
Currently you have to pass in a logical vector as long as `nrow(geneSets(gdb))` to filter out gene sets from a GeneSetDb. I am imagining an NSE (and tidyselect-compatible) way to...
For some reason, the scores provided by the gsva and plage methods are *just a bit off* when run directly through the `GSVA` package vs the `do.scoreSingleSamples.gsva` wrapper. Explore this...
The `getPantherGeneSetDb` function throws an error when I try to reproduce the example provided in the vignette. No object is returned: ```r library(multiGSEA) goslimdb
We are hacking together the expected `*.rds` name for the MSigDB `GeneSetDb.*` objects based on version, species, and identifiers in the [`getMSigGeneSetDb` function](https://github.com/lianos/multiGSEA/blob/1421828672f1072ff0a9a0cd973b58c92f72a510/R/msigdb-broad.R#L74). The current implementation is flimsy and can...
It should be relatively simple to add [singscore](https://bioconductor.org/packages/release/bioc/vignettes/singscore/inst/doc/singscore.html) as a `method` option in `scoreSingleSamples`. The package was added as part of the Bioconductor 3.7 release. The accompanying paper/preprint can be...
This handles dense and sparse matrices, and other goodies. It returns a list that largely looks like the return value from `base::svd`