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Version 0.6

AcidGSEA 0.6.0 (2021-02-17)

Major changes:

  • Reworked and simplified NAMESPACE and package dependencies, following basejump v0.14 release series update.
  • Removed BiocParallel as a required import.

AcidGSEA 0.6.1 (2021-03-04)

New functions:

  • prepareGeneSetFiles: MSigDb utility function for easy matching of default GMT gene files to use for GSEA. Matches the symbol files by default.

Major changes:

  • RankedList and FGSEAList method support has been improved for minimal DESeqResults and DataFrame objects. These approaches are intended primarily for analysis of files from collaborators where we don’t necessarily have the complete set of DESeq2 analysis files, and therefore cannot construct a DESeqAnalysis object.

Minor changes:

  • RankedList now supports keyType, which defaults to gene name (a.k.a. symbol), but now also supports original gene identifier. This alternative option is useful when working with the clusterProfiler package and is used in the bcbioRNASeq template.

AcidGSEA 0.6.2 (2021-03-16)

Minor changes:

  • Updated basejump dependencies.
  • Resaved example fgsea object (FGSEAList).
  • Updated unit tests.

AcidGSEA 0.6.3 (2021-06-29)

Minor changes:

  • RankedList: Improved column name sanitization and handling for input DESeqResults object, avoiding conflicts with Gene2Symbol object.
  • Improved unit tests to no longer rely on gene sets saved in ~/msigdb.

AcidGSEA 0.6.4 (2021-07-21)

Minor changes:

  • RankedList: Improved handling of duplicate Entrez gene identifiers, such as is the case in the bcbioRNASeq F1000 example dataset.
  • Reorganized and consolidated S4 method exports.