# 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()`