theme_paperwhitefrom minimalism package.
BPPARAM, to match Bioconductor. Also now reexporting
gseaminimal working example dataset, for unit testing.
theme_paperwhite. Now reexporting this function.
contrastNames: Accessor functions for pathway (e.g. MSigDb) and differential expression contrast names.
enrichedmethod support for FGSEAList class. Useful for returning a list directionally significant pathways, per contrast. Primarily intended for use at the moment with
plotEnrichedUpset: Utility function that makes it easy to compare enrichment groups across contrasts, via an UpSet plot.
combinemethod support for
FGSEAList, allowing us to easily combine GSEA results from multiple datasets. Primarily intended for downstream visualization using an UpSet plot (see
plotEnrichedUpsethave been updated to return per collection (e.g. hallmark gene set), which makes more sense. We don’t want to visualize overlap across collections, since these are often completely different classes (e.g. c1-c7 will never have overlap).
convertToHuman, which allows for easy ortholog conversion to HUGO (HGNC) identifiers.