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Version 0.6

DESeqAnalysis 0.6.0 (2022-05-06)

Major changes:

  • Package now requires R 4.2 / Bioconductor 3.15.

Minor changes:

  • Reworked internal droplevels calls against SummarizedExperiment using new droplevels2 approach, which provides better compatibility with Bioconductor 3.15 release.
  • Reworked internal handoff to ggplot, using as.data.frame coercion instead of as_tibble.

DESeqAnalysis 0.6.1 (2022-05-18)

Minor changes:

  • Hardened resultsTables and topTables to work with minimal DESeqDataSet that doesn’t contain gene names and additional metadata in rowData.
  • Improved plotDEGStackedBar and plotDEGUpset to early return with alert warning for objects without DEGs.
  • Resaved example objects and added new deseqMinimal object, that contains an unusually small DESeqDataSet without metadata, which is useful for testing edge case handling in our plotting functions.
  • Updated lintr checks and migrated to testthat 3e for unit tests.
  • Now consistently using Map instead of mapply, as recommended by lintr.
  • plotBaseMean now longer exporting integer method – using internally only.

DESeqAnalysis 0.6.2 (2022-05-24)

Major changes:

  • Reworked and simplified topTables as markdownTables.
  • Simplified resultsTables return to always return as DataFrameList containing subset DESeqResults. Previously tbl_df option was available, but this has been removed in favor of Bioconductor S4Vectors support instead.
  • Improved code coverage of export, markdownTables, and resultsTables, to ensure that we never drop rownames.

DESeqAnalysis 0.6.3 (2022-05-25)

Minor changes:

  • Removed deprecated plotMeanAverage and apeglmContrast functions from NAMESPACE, to avoid collisions with updates in bcbioRNASeq package.

DESeqAnalysis 0.6.4 (2022-06-09)

Minor changes:

  • Improved Windows CI compatibility, using tempdir2 and unlink2.

DESeqAnalysis 0.6.5 (2022-08-30)

Minor changes:

  • Updated package to roxygen2 7.2.1.
  • results: Now defaults to quiet = TRUE by default, to reduce the amount of message spam in bcbioRNASeq R Markdown templates.

DESeqAnalysis 0.6.6 (2022-10-25)

Major changes:

  • export: Reduced the number of exported methods, to match the new conventions defined by pipette. Note that con is now required instead of dir for the target directory.

Minor changes:

  • Tightened up dependency requirements.
  • Improved consistency of internal goalie boolean functions.

DESeqAnalysis 0.6.7 (2023-02-09)

Minor changes:

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

DESeqAnalysis 0.6.8 (2023-04-28)

Major changes:

  • Reworked prepareTximportFiles to work on a directory instead of files.

Minor changes:

  • Now classing on DFrame instead of DataFrame virtual class consitently.
  • Resaved example deseq and deseqMinimal objects.
  • Removed unused matchMetadataToFiles function.

DESeqAnalysis 0.6.9 (2023-07-13)

Major changes:

  • Updated dependencies to R 4.3 / Bioconductor 3.17.

Minor changes:

  • Removed internal calls to basejump package, which has been changed to a meta-package of Acid Genomics packages, without any exports in NAMESPACE. This has been corrected inside of prepareTximportFiles to correctly reference the methods exported in syntactic package.

DESeqAnalysis 0.6.10 (2023-07-25)

New functions:

  • sanitizeTximportIdentifiers: New utility function for sanitizing malformed transcript identifiers returned when importing salmon data generated against GENCODE-aligned BAM files. We hit this edge case when processing Nanopore samples using guppy to minimap2 to BAM with samtools. This edge case has also be observed when importing kallisto data aligned against GENCODE, which also doesn’t currently handle transcript identifier sanitization correctly.

DESeqAnalysis 0.6.11 (2023-07-25)

Minor changes:

  • sanitizeTximportIdentifiers: Fixed typo in identifier check pattern.

DESeqAnalysis 0.6.12 (2023-08-15)

Minor changes:

  • Reworked internal ggplot2 code to use data pronouns (.data) instead of rlang syntactic sugar (!!/sym).
  • Using updated AcidPlots functions: acid_scale_color_discrete instead of autoDiscreteColorScale and acid_discrete_coord_flip instead of acid_coord_flip.