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Version 0.3

acidgsea 0.3.0 (2020-05-24)

Major changes:

  • FGSEAList: Converted function to an S4 generic. Previously the main arguemnt was named rankedList, but this has been renamed to object. A RankedList object can still be passed in as the first object in the function call. This change was necessary for adding GSEA support in pointillism single-cell RNA-seq analysis toolkit.

Minor changes:

  • RankedList: Added support for DataFrame class, which is used inside pointillism package update.
  • RankedList: Added gene2symbol argument support for matrix model. Using this for cluster matrix in pointillism for scRNA-seq using output from edgeR (or DESeq2) for per-cluster marker analysis.

acidgsea 0.3.1 (2020-07-24)

New functions:

  • plotGeneSet: Split out internal gene set plotting code used previously in plotEnrichedGeneSets. This is a modified variant of fgsea::plotEnrichment that allows for additional color customization.

Major changes:

  • Updated minimum R dependency to 4.0.
  • plotEnrichedGeneSets: Now calls new plotGeneSet function internally.

Minor changes:

  • Removed UpSetR dependency, based on update to AcidPlots package.
  • Removed plotCounts method, in favor of plotHeatmap usage.

acidgsea 0.3.2 (2020-08-05)

Major changes:

  • Simplified internal handling of alpha (now consistently referfed to as “alphaThreshold”) and nesThreshold.
  • Added alphaThreshold and nesThreshold S4 generic support.
  • These name chanages better match the syntax used in DESeqAnalysis v0.3.