Various scripts to change fasta files (i.e. headers, chromosome separators, etc...)
matrix.py converts TADbit matrix files (.mat) to BUTLRTools format
bismark_chr_cov.py adds 'chr' to bismark .cov files that were aligned without 'chr' in the reference genome
basemods_separator.py parses GFF files based on base modification (i.e. PacBio modifications - m6A, m4C etc...)
juicer_2_tadbit.py takes juicer_tools dump dense matrix and appends chromosome column and bin position, making file compatible with TADbit find.tads()
singlecell_DamID.py takes scDamID data from Kind et al., 2015 Cell and aggregates data into bedgraph format using numpy
domain_caller.py takes bedgraph files and calls megabase sized domains
translocation_hic.py takes Hi-C data in cooler format and looks for regions where trans (interchromosomal) interactions are higher than median of cis (intrachromosomal) interactions