Changelog • extraChIPs

Submitted to Bioconductor

Bugfix so as_tibble() respects original column names

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()

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

Added makeConsensus() and updated vignette

Added mergeBySig()

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

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

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

Added using coverage to makeConsensus()

Changed labelling strategy for plotPie()

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()

Added plotPairwise() and addDiffStatus()

Added mapGrlCols()

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

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

Added bed format to importPeaks()

Added defineSeqinfo()

Added plotGrlCol()

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

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

Added the DESeq2 Wald statistic to options for fitAssayDiff()

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

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