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Version 0.8

AcidGSEA 0.8.0 (2022-05-06)

Major changes:

  • Package now requires R 4.2 / Bioconductor 3.15.
  • Compatibility fixes for breaking changes in pipette package.

AcidGSEA 0.8.1 (2022-05-24)

Major changes:

  • Reworked topTables as markdownTables, following updated conventions used in other Acid Genomics packages, such as AcidMarkdown and DESeqAnalysis.

Minor changes:

  • Updated lintr checks and testthat unit tests.

AcidGSEA 0.8.2 (2022-05-26)

Major changes:

  • RankedList: Improved keyType support, adding back "geneId", and "ensemblId". Simplified internal code for unlisting nested Entrez identifier keys and ensuring they map 1:1 by oldest identifier.
  • RankedList: Function now looks inside geneId and checks against provider metadata defined in rowRanges, in the event that ensemblId or ensemblId mcols are not defined, but the key is in Ensembl or Entrez format.
  • RankedList: In the event the user requests keyType of "geneId" or "ensemblId", we now also call stripGeneVersions to sanitize the gene identifiers to remove gene versions.

AcidGSEA 0.8.3 (2022-06-09)

Minor changes:

  • Improved support for Windows CI checks, using tempdir2 and unlink2.

AcidGSEA 0.8.4 (2022-08-17)

Major changes:

  • FGSEAList: Simplified input to use recommended defaults for fgsea passthrough. Note that fgsea now uses fgseaMultilevel by default in Bioconductor 3.15. Object class checks have been updated to reflect this breaking change.

Minor changes:

  • RankedList: Fix for ensemblId handling as input.
  • Resaved example fgsea object.

AcidGSEA 0.8.5 (2022-08-31)

Major changes:

  • RankedList Relaxed the internal thresholds for acceptable gene identifier mapping thresholds. Previous cutoffs were a bit too strict and could result in errors with acceptable datasets.
  • export: Simplified S4 method to class with con and format arguments defined as required character and missingOrNULL, respectively. Improved the documentation to denote that user should specify a directory as con, and either "csv" or "tsv" as the desired output format.

Minor changes:

  • Updated roxygen2 documentation.
  • Resolved any Markdown lints using markdownlint.

AcidGSEA 0.8.6 (2022-10-25)

Major changes:

  • Hardened package dependency requirements.
  • export: Restricting methods, following conventions now defined in pipette 0.10.0 update.
  • Using hasDuplicates internally from goalie.

AcidGSEA 0.8.7 (2023-02-09)

Minor changes:

  • Updated dependencies to Bioconductor 3.16.
  • Migrated requireNamespaces import from AcidBase to goalie.

AcidGSEA 0.8.8 (2023-04-28)

Major changes:

  • Reworked handling of NCBI (Entrez) gene identifiers.
  • Now classing on DFrame instead of DataFrame virtual class, where applicable.
  • Also classing on GRanges directly instead of GenomicRanges virtual class, where applicable.

AcidGSEA 0.8.9 (2023-08-15)

Minor changes:

  • Now requiring R 4.3 / Bioconductor 3.17.
  • Reworked internal ggplot2 code to use data pronouns instead of rlang syntactic sugar.
  • Updated NAMESPACE related to AcidPlots.