PYHR

A custom genomics and epigenomics package

Function Overview

Dependencies

requirement

• 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/]

Changelog

• 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]