Public repository of additional scripts used in our expanded alphabet manuscript.
These include:
- run_cytomod_TFBS_pipeline.sh: used along with the below scripts, to construct (K562) modified genomes
- computePseudocountForKLequality.py, makeRegionBaseFreqPlots.sh, output5mC5hmCModBaseBEDsAtThreshold.py, and run_hypothesis_tests.sh.
- processDataAndPlot.py: used to create our main scored data and creates swarm plots
- run_matrix-clustering-specific_TFs.sh: used to run RSAT matrix-clustering
- gen_treemaps.py: used to create treemaps, of scored and clustered hypothesis pairs
- call_peaks-MACS-uncalibrated-short_reads.sh: used to call peaks for our CUT&RUN datasets