NEWS

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extraChIPs 1.9.6

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

extraChIPs 1.7.7

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

extraChIPs 1.7.6

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

extraChIPs 1.5.14

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

extraChIPs 1.5.13

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

extraChIPs 1.5.12

• Added plotGrlCol()

extraChIPs 1.5.11

• Added defineSeqinfo()

extraChIPs 1.5.10

• Added bed format to importPeaks()

extraChIPs 1.5.8

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

extraChIPs 1.5.7

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

extraChIPs 1.5.6

• Added mapGrlCols()

extraChIPs 1.5.5

• Added plotPairwise() and addDiffStatus()

extraChIPs 1.4.2

• 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()

extraChIPs 1.3.9

• Changed labelling strategy for plotPie()

extraChIPs 1.3.8

• Added using coverage to makeConsensus()

extraChIPs 1.3.7

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

extraChIPs 1.3.6

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

extraChIPs 1.3.5

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

extraChIPs 1.3.4

• Added mergeBySig()

extraChIPs 1.1.5 (2022-10-11)

• Added makeConsensus() and updated vignette

extraChIPs 1.1.3 (2022-08-01)

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

extraChIPs 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()

extraChIPs 1.1.1 (2022-06-01)

• Bugfix so as_tibble() respects original column names

extraChIPs 0.99.0 (2022-03-28)

• Submitted to Bioconductor