Changelog

Source: NEWS.md

extraChIPs 1.12.1

Bug Fixes

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

extraChIPs 1.11.2

Changes

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

extraChIPs 1.11.1

No user-facing changes

extraChIPs 1.11.0

Bioconductor 3.20 release

extraChIPs 1.9.6

New Features

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

extraChIPs 1.7.7

Improvements

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

extraChIPs 1.7.6

New Features

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

extraChIPs 1.5.14

Improvements

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

extraChIPs 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()

extraChIPs 1.5.12

New Features

• Added plotGrlCol()

extraChIPs 1.5.11

New Features

• Added defineSeqinfo()

extraChIPs 1.5.10

Improvements

• Added bed format to importPeaks()

extraChIPs 1.5.8

Improvements

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

extraChIPs 1.5.7

Improvements

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

extraChIPs 1.5.6

New Features

• Added mapGrlCols()

extraChIPs 1.5.5

New Features

• Added plotPairwise() and addDiffStatus()

extraChIPs 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()

extraChIPs 1.3.9

Improvements

• Changed labelling strategy for plotPie()

extraChIPs 1.3.8

Improvements

• Added coverage option to makeConsensus()

extraChIPs 1.3.7

New Features

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

extraChIPs 1.3.6

New Features

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

Improvements

• Expanded arguments for plotSplitDonut()

extraChIPs 1.3.5

New Features

• Added plotSplitDonut()

Bug Fixes

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

extraChIPs 1.3.4

New Features

• Added mergeBySig()

extraChIPs 1.1.5

New Features

• Added makeConsensus() and updated vignette

extraChIPs 1.1.3

New Features

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

extraChIPs 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()

extraChIPs 1.1.1

Bug Fixes

• Fixed as_tibble() to respect original column names

extraChIPs 0.99.0

Major Changes

• Submitted to Bioconductor