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NEWS.md

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Changes in version 0.99.0 (2022-03-28)

  • Submitted to Bioconductor

Changes in version 1.1.1 (2022-06-01)

  • Bugfix so as_tibble() respects original column names

Changes in version 1.1.2 (2022-07-22)

  • Added collapseTranscripts = "auto" as the default for plotHFGC()
  • getProfileData() now returns log2 transformed data by default
  • getProfileData() now uses bplapply() internally
  • Bugfixes for plotPie(), distinctMC() colToRanges() and stitchRanges()

Changes in version 1.1.3 (2022-08-01)

  • Added plotOverlaps() for generation of Venn Diagrams and ComplexUpset plots

Changes in version 1.1.5 (2022-10-11)

  • Added makeConsensus() and updated vignette

Changes in version 1.3.4 (22-12-20)

  • Added mergeBySig()

Changes in version 1.3.5 (23-01-31)

  • Added plotSplitDonut()
  • Bugfix in plotAssayDensities() and plotAssayRle() along with enabling plotting by group

Changes in 1.3.6 (23-03-12)

  • Expanded arguments for plotSpliDonut()
  • Added mergeByHMP() for merging overlapping windows using the harmonic mean p

Changes in 1.3.7 (23-03-20)

  • Added plotAssayHeatmap()
  • Added fitAssayDiff() and added coercion of TopTags objects

Changes in 1.3.8 (23-03-20)

  • Added using coverage to makeConsensus()

Changes in 1.3.9 (23-04-10)

  • Changed labelling strategy for plotPie()

Changes in 1.4.2 (23-06-20)

  • Added Fixed-width vignette & edited sliding window
  • Added se and peaks as example data for man pages and vignettes
  • Included defineRegions()
  • Enabled plotHFCG() without Ideogram tracks
  • Enabled use of offsets for normalisation in fitAssayDiff()

Changes in 1.5.5 (23-06-28)

  • Added plotPairwise() and addDiffStatus()

Changes in 1.5.6 (23-07-01)

  • Added mapGrlCols()

Changes in 1.5.7 (23-07-08)

  • Matched DiffBind and csaw settings for fitAssayDiff()
  • Added min_win to all merging functions
  • Added n_max to getProfileData()

Changes in 1.5.8 (23-07-14)

  • Added control of side-axis label position for plotProfileHeatmap()
  • Added option to return merged key-value ranges for mergeByHMP()

Changes in 1.5.10 (23-08-11)

  • Added bed format to importPeaks()

Changes in 1.5.11 (23-08-26)

  • Added defineSeqinfo()

Changes in 1.5.12 (23-08-30)

  • Added plotGrlCol()

Changes in 1.5.13 (23-09-24)

  • Added handling of unquoted column names to most plotting functions
  • Added passing of specific columns to dualFilter
  • Added drop to addDiffStatus

Changes in 1.5.14 (23-09-24)

  • Added p_mu0 to output of fitAssayDiff()
  • Added respectLevels and filtering to plotProfileHeatmap()

Changes in 1.7.6

  • Added the DESeq2 Wald statistic to options for fitAssayDiff()

Changes in 1.7.7

  • Added merge_within to makeConsensus() for better handling when method = "coverage"

Changes in 1.9.6

  • Added the function centrePeaks() to recentre peaks using any files with coverage