A custom genomics and epigenomics package
- Python packages
- natsort
- intervaltree
- argparse
- path
- pandas
- numpy
- biopython
- gffutils
- gzip
- rich
- scipy
- cooler
- cooltools
- bioframe
- cytoolz
- matplotlib
- pysam
- coolpuppy
- Executable programs
- ice
- build_matrix [from HiC-Pro/scripts/]
-
v0.4.6
- DEBUG [utils.kit compare_md5]
- Rename [hic.utils] to [hic.base]
- Rename [utils.Bam StatMappedRate] to [utils.Bam StatMappedRateHisat2]
-
v0.4.5
- DEBUG [threeD.loop read_loop AND findOverlapLoops]
- Rename [utils.kit CheckMd5] to [utils.kit CheckMD5]
-
v0.4.4
- New function [hic.matrix Dump2Matrix]
-
v0.4.3
- DEBUG [utils.kit CheckMd5]
- DEBUG [hic.loop findOverlapLoops]
- New function [hic.utils DownsampleValid]
-
v0.4.1
- Rename [PYHR.3D] to [PYHR.threeD]
- New module [threeD.base]
- New function [threeD.TAD ATA]
- Move [threeD.AB read_cool] to [threeD.base read_cool]
- Move [threeD.AB readGCfile] to [threeD.base readGCfile]
- Move [threeD.AB getResolution] to [threeD.base getResolution]
- Move [threeD.AB countGC] to [threeD.base countGC]
- Move [threeD.AB filter_chrom] to [threeD.base filter_chrom]
- Move [threeD.AB calExpectedCis] to [threeD.base calExpectedCis]
-
v0.3.4
- New function [3D.AB CountsGC]
- New function [3D.AB cooltoolsAB]
- New function [3D.AB plotSaddle]
- New function [3D.AB ABStremgth]
- DEBUG [3D.TAD boundaries2bed]
- DEBUG [utils.kit CheckMd5]
-
v0.3.3
- Update [hic.utils statHiCPro] and [utils.kit CheckMd5]
- Debug [3D.TAD boundaries2bed]
-
v0.3.2
- move [rna.utils StatHisat2MappedRate] to [utils.bam StatHisat2MappedRate]
- rename [utils.bam StatHisat2MappedRate] to [utils.bam StatMappedRate]
- DEBUG [utils.bam StatMappedRate]
-
v0.3.1:
- move [3D.matrix] to [hic.matrix]
- New module [3D.TAD]; new function [3D.TAD boundaries2bed]
- rename [hic.matrix CreateMatrix] to [hic.matrix CreateNNMatrix]
- rename [hic.utils hicprostats] to [hic.utils statHiCPro]