Changes in version 1.12.1                        

Bug Fixes

  - Patched for ggplot2 v4.0.0
  - Switched to SimpleUpset for Upset plots

                       Changes in version 1.11.2                        

Changes

  - Changed handling of arguments in plotting functions, setting NULL as
    the primary default value

                       Changes in version 1.11.0                        

Bioconductor 3.20 release

                        Changes in version 1.9.6                        

New Features

  - Added centrePeaks() to recentre peaks using any files with coverage

                        Changes in version 1.7.7                        

Improvements

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

                        Changes in version 1.7.6                        

New Features

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

                       Changes in version 1.5.14                        

Improvements

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

                       Changes in version 1.5.13                        

Improvements

  - Added handling of unquoted column names to most plotting functions
  - Added passing of specific columns to dualFilter()
  - Added drop argument to addDiffStatus()

                       Changes in version 1.5.12                        

New Features

  - Added plotGrlCol()

                       Changes in version 1.5.11                        

New Features

  - Added defineSeqinfo()

                       Changes in version 1.5.10                        

Improvements

  - Added bed format to importPeaks()

                        Changes in version 1.5.8                        

Improvements

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

                        Changes in version 1.5.7                        

Improvements

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

                        Changes in version 1.5.6                        

New Features

  - Added mapGrlCols()

                        Changes in version 1.5.5                        

New Features

  - Added plotPairwise() and addDiffStatus()

                        Changes in version 1.4.2                        

New Features

  - Added fixed-width vignette and edited sliding window vignette
  - Added se and peaks as example data for man pages and vignettes
  - Added defineRegions()

Improvements

  - Enabled plotHFGC() without Ideogram tracks
  - Enabled use of offsets for normalisation in fitAssayDiff()

                        Changes in version 1.3.9                        

Improvements

  - Changed labelling strategy for plotPie()

                        Changes in version 1.3.8                        

Improvements

  - Added coverage option to makeConsensus()

                        Changes in version 1.3.7                        

New Features

  - Added plotAssayHeatmap()
  - Added fitAssayDiff() and coercion of TopTags objects

                        Changes in version 1.3.6                        

New Features

  - Added mergeByHMP() for merging overlapping windows using the
    harmonic mean p-value

Improvements

  - Expanded arguments for plotSplitDonut()

                        Changes in version 1.3.5                        

New Features

  - Added plotSplitDonut()

Bug Fixes

  - Fixed bug in plotAssayDensities() and plotAssayRle() and enabled
    plotting by group

                        Changes in version 1.3.4                        

New Features

  - Added mergeBySig()

                        Changes in version 1.1.5                        

New Features

  - Added makeConsensus() and updated vignette

                        Changes in version 1.1.3                        

New Features

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

                        Changes in version 1.1.2                        

Improvements

  - Added collapseTranscripts = "auto" as default for plotHFGC()
  - getProfileData() now returns log2 transformed data by default
  - getProfileData() now uses bplapply() internally

Bug Fixes

  - Fixed bugs in plotPie(), distinctMC(), colToRanges(), and
    stitchRanges()

                        Changes in version 1.1.1                        

Bug Fixes

  - Fixed as_tibble() to respect original column names

                       Changes in version 0.99.0                        

Major Changes

  - Submitted to Bioconductor