# 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
