DESeqAnalysis 0.3.0 (2020-08-05)

Major changes

  • DESeqAnalysis object now supports stashing of threshold metadata:
    • alphaThreshold.
    • lfcShrink: whether to use (adaptie) shrunken LFC values or not.
    • lfcThreshold (for post-hoc cutoffs).
    • baseMeanThreshold. These are defined in the metadata slot of the object and can be accessed/ modified with corresponding S4 generics.
  • Updated default differential expression R Markdown template to support additional parameters:
    • alpha_threshold
    • base_mean_threshold
    • contrast_samples
    • lfc_shrink
    • lfc_threshold

Minor changes

  • Switched to cli package for more informative messages.

DESeqAnalysis 0.3.1 (2020-08-07)

Minor changes

  • Adjusted minimum dependency versions so package will build on bioconda.

DESeqAnalysis 0.3.2 (2020-08-13)

Minor changes

  • Added i argument support to degPerContrast, and the plotting functions plotDEGUpset and plotStackedBar, which call degPerContrast internally. This allows the user to pick specific contrasts of interest to plot.
  • plotDEGStackedBar: Now allowing the user to pick only up- or down-regulated genes, which can be useful.
  • Bug fix for apeglmResults cli display code.

DESeqAnalysis 0.3.3 (2020-08-17)

Minor changes

  • apeglmResults: Simplified default arguments and disabled ... passthrough to lfcShrink, which is a bit confusing. Note that DESeq and lfcShrink are now called internally with parallel = TRUE.

DESeqAnalysis 0.3.4 (2020-08-18)

New functions

  • degIntersection: Utility function that will return the number of times a DEG is detected across contrasts.

DESeqAnalysis 0.3.5 (2020-08-18)

Minor changes

  • degIntersection: Bug fix for column names not returning as expected.

DESeqAnalysis 0.3.6 (2020-08-25)

Minor changes

  • plotDEGPCA: Updated internal title and subtitle handoff to plotPCA.
  • Quieted down messages in plotDEG* functions. This information is shown in the plots and doesn’t need to be messaged.

DESeqAnalysis 0.3.7 (2020-09-18)

Minor changes

  • results: Bug fix for logical check on lfcShrink return. The internal use of identical here is too strict, as lfcShrink can return cause attribute from goalie.
  • lfcShrink: Hardened logical return, ensure goalie cause attribute removal.

DESeqAnalysis 0.3.8 (2020-09-21)

Minor changes

  • Migrated extra mode internal code from resultsTables directly into results, so we can hand-off to new methods defined in acidgsea package that depend on DESeqResults object (i.e. geneSetResults). The resultsTables function still behaves the same as previous releases.
  • plotDEGStackedBar: Added support for orderBySize argument.
  • degPerContrast: Removed unnecessary n argument; use return instead.

DESeqAnalysis 0.3.9 (2020-10-08)

Minor changes

  • Updated package dependency version requirements.