# 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