pfgsea 0.1.0 (2019-03-23)

pfgsea 0.1.1 (2019-04-01)

Minor changes

  • NAMESPACE updates to reflect changes in basejump package.
  • Now importing theme_paperwhite from minimalism package.

pfgsea 0.1.2 (2019-04-10)

Major changes

  • Deleted list to FGSEAList coercion method.

Minor changes

  • pfgsea: Renamed bpparam argument to BPPARAM, to match Bioconductor. Also now reexporting BiocParallel::bpparam.
  • Added gsea minimal working example dataset, for unit testing.
  • Added documentation working examples, using gsea data.
  • Updated NAMESPACE for theme_paperwhite. Now reexporting this function.

pfgsea 0.1.3 (2019-04-17)

Minor changes

  • Updated Travis CI configuration to use rnaseq Docker image.
  • Miscellaneous documentation improvements.

pfgsea 0.1.4 (2019-04-23)

Minor changes

  • Switch to importing graphics code from acidplots package instead of now defunct minimalism package. Default ggplot2 theme has been renamed from theme_paperwhite to acid_theme_light.

pfgsea 0.1.5 (2019-04-25)

Minor changes

  • S4 generic reexport documentation fixes.

pfgsea 0.1.6 (2019-04-29)

New functions

  • pathwayNames, contrastNames: Accessor functions for pathway (e.g. MSigDb) and differential expression contrast names.
  • enriched method support for FGSEAList class. Useful for returning a list directionally significant pathways, per contrast. Primarily intended for use at the moment with plotEnrichedUpset.
  • plotEnrichedUpset: Utility function that makes it easy to compare enrichment groups across contrasts, via an UpSet plot.

Major changes

  • Added combine method support for FGSEAList, allowing us to easily combine GSEA results from multiple datasets. Primarily intended for downstream visualization using an UpSet plot (see plotEnrichedUpset).

Minor changes

  • Improved show method support for FGSEAList, showing pathwayNames and contrastNames more clearly.

pfgsea 0.1.7 (2019-04-30)

Major changes

  • Reworked language to use “collection” consistently instead of mixing/matching “geneSet” and “pathway”, which isn’t appropriate. Relevant function arguments have been updated to reflect this change.
  • Now exporting collectionNames instead of pathwayNames.
  • enriched and plotEnrichedUpset have 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).