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Version 0.5

DESeqAnalysis 0.5.0 (2022-04-15)

New functions:

  • plotContrastScatter: Visualize expression between numerator and denominator for a contrast of interest.
  • plotLFC: Plot log2 fold change distributions for all contrasts in the DESeq2 analysis.

Major changes:

  • Updated dependencies to R 4.1 / Bioconductor 3.14.
  • export: Updated method to inherit BiocIO conventions now used in basejump, which now rely on con argument.
  • Added as.DESeqDataSet and as.DESeqTransform coercion methods.

Minor changes:

  • plotPCA: Tightned up method export to only work on DESeqAnalysis object, so we don’t conflict with DESeqTransform method defined in DESeq2.
  • plotVolcano: Hardened against edge case where visualization of a specific gene is requested, but contains a censored adjusted P value.
  • Updated example deseq object.
  • Added basejump as a library load in DE template.
  • contrastSamples: Improved documentation.
  • Package code is now formatted according to styler conventions.