NEWS.md

In steveped/extraChIPs: Additional functions for working with ChIP-Seq data

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"

steveped/extraChIPs documentation built on May 12, 2024, 2:55 p.m.