# Change log
All notable changes to this project will be documented in this file. Here we
will document changes to major new releases only (not point releases).
## [1.3.3] -- 2022-01-27
- Updated cumulative distribution feature overlap plots and description
## [1.3.2] -- 2022-01-20
- Bioconductor released new version
- Cell specificity plots are now more generic signal summary plots - the calc function is now "calcSummarySignal", plot function "plotSummarySignal"
- Added calculation of Chi-square p-values of expected partitions as default output of "calcExpectedPartitionsRef"
- Chi-square p-values are now optionally shown as stars on top of each partition output by "plotExpectedPartitions"
- Chromosome distribution calculations have been optimized to substantially reduce running time
- Default plotting of neighbor distance now includes an X-axis log scale to account for outliers more intuitively
- Corrected plotting of partition overlap for multiple region sets - now sums to 100 by group
- Intro vignette has been updated to include "calcSummarySignal" and "plotSummarySignal" functions along with expected partitions p-values calculation and updated X-axis scale of neighbor dist plots
## [1.1.2] -- 2020-07-07
- Added functions to calculate and plot dinucleotide frequencies
## [1.1.1] -- 2020-06-03
- Package now on Bioconductor under 1.0.0 (dev version 1.1.0) - bump to 1.1.1
- Added sorting option to feature distance plot
- Added stack bar option to partition plots
- Fixed ordering of chromosome distribution
- Added possibility to calculate proportional overlap in partition plots
- Expected partition distribution now calculated based on annotation class object sizes
- Improved definition of introns in gene partition lists
- Improved memory and time performance
- In full power vignette added option to add custom annotation classes in partition plots
- Added functions to create annotations out of GTF files
- New vignette - how to build custom reference data
## [0.99.0] -- 2020-05-26
- Update R version to 4.0
- Bioconductor submission
## [0.8] -- 2020-05-20
- Added tiled version to feature distance plot
- Added percentage plots to feature distances
- Reduced data shipped with package
- Reduced verbosity of calc functions
- Simplified functions for calculating overlaps
- Added UTRs to gene models
- Moved data producing functions to data-raw
- Improved 'full power' vignette
- Bug fixes for edge cases, like plotting distribution with only one value
## [0.7] -- 2020-04-11
- Revamped TSS distance distribution plots to better reflect the scale of distances
- Added new versions of partition plots
- Added new cell-type specificity plot
- Added new quantile-trimmed histogram for width distribution plots
- Added new unit tests and updated coding style for bioconductor
## [0.6] -- 2019-09-20
- Added functions to calculate GC content
## [0.5] -- 2018-04-30
- Built-in data added for mm9 assembly
- Functions can now accept TxDb objects, in addition to EnsDb objects
## [0.4] -- 2018-04-05
- Add partition plots
## [0.3] -- 2018-03-05
- Revamp all function names, make functions more parallel and modular
- Dramatic increase in speed for feature distance plots
## [0.2] -- 2018-03-02
- Make bins the same size, instead of having the same number of bins per chrom
- Divest dependency on BSGenome and ensembldb by integrating basic data
## [0.1] -- 2018-02-01
- First version released