- Meth_Seg now allows for filtering which read-groups to be used in the segmentation (parameter
--read_groups_to_include) - Multiple bugfixes
- Implemented Fisher-Exact test for 2-sample testing and Chi-squared test for multi-sample testing (with Fisher exact as a post-hoc test)
- Implemented post-hoc testing and reporting for multi-sample tests
- Multiple bugfixes and performance improvements
- First release of PycoMeth 2.0 using the MetH5 as an input.
- Meth_Seg is now a firm component of PycoMeth, allowing for de novo methylaiton segmentation
- Additional testing modes: paired-CpG methylation rate testing as well as unpaired read-methylation rate testing
- CpG_Aggregate and Interval_Aggregate removed as these are no longer necessary since random access to methylation calls is possible in the MetH5 Format
- Meth_Comp can now be computed on multiple CPUs.
- Switch from orca to kaleido for static export
- Export summary of intervals in table file for all intervals and not just for top hits
- Add new plot for distance between CpG islands and closest tss
- Speed improvement to Comp_report
- Add interactive API to Comp_report
- Add ability to export static plots using orca
- Add tabular text reports to Comp_report
- Add (default) option to write out all the intervals in Meth_Comp with reasons why excluded or included in DM analysis
- Improve Comp_report summary table and include new fields from Meth_Comp
- Tidy output folder structure for reports generated by meth_report
- Add Chromosome ideogram plot to summary report
- A fasta reference is now required to run Comp_Report
- General improvement of logging message output
- Implement fancy color logger
- Add position tracking within intervals
- Add Comp_Report module to generate HTML reports of significant candidates
- Deep refactoring of Freq_meth_calculate to Aggregate
- Major doc update including doc folders reorganisation
- Implement autodoc from docstring
- Fix and test CLI