Repositories list

• deeptools4_benchmark

  Public
  repo for benchmarking, comparison, test data and reference construction for the 25 remake.

  Python

  •00 forks in deeptools/deeptools4_benchmark•00 stars in deeptools/deeptools4_benchmark•00 issues in deeptools/deeptools4_benchmark•00 pull requests in deeptools/deeptools4_benchmark•Updated Oct 15, 2026Oct 15, 2026

• deepTools

  Public
  Tools to process and analyze deep sequencing data.

  pythonbioinformaticsrna-seq+ 3

  pythonbioinformaticsrna-seqgenomicsngschip-seq

  Python

  •

  MIT License

  •221221 forks in deeptools/deepTools•769769 stars in deeptools/deepTools•8686 issues in deeptools/deepTools•1111 pull requests in deeptools/deepTools•Updated Oct 15, 2026Oct 15, 2026

• pyBigWig

  Public
  A python extension for quick access to bigWig and bigBed files

  bigwigbigbedbioinfomatics

  bigwigbigbedbioinfomatics

  C

  •

  MIT License

  •5757 forks in deeptools/pyBigWig•252252 stars in deeptools/pyBigWig•99 issues in deeptools/pyBigWig•11 pull request in deeptools/pyBigWig•Updated Oct 11, 2026Oct 11, 2026

• pyGenomeTracks

  Public
  python module to plot beautiful and highly customizable genome browser tracks

  Python

  •

  GNU General Public License v3.0

  •127127 forks in deeptools/pyGenomeTracks•905905 stars in deeptools/pyGenomeTracks•2222 issues in deeptools/pyGenomeTracks•44 pull requests in deeptools/pyGenomeTracks•Updated Oct 3, 2026Oct 3, 2026

• HiCExplorer

  Public
  HiCExplorer is a powerful and easy to use set of tools to process, normalize and visualize Hi-C data.

  pythonbioinformaticsgenomics+ 3

  pythonbioinformaticsgenomicsgalaxyhicchromosome-conformation-capture

  Python

  •

  GNU General Public License v3.0

  •7676 forks in deeptools/HiCExplorer•280280 stars in deeptools/HiCExplorer•160160 issues in deeptools/HiCExplorer•00 pull requests in deeptools/HiCExplorer•Updated Sep 24, 2026Sep 24, 2026

• py2bit

  Public
  A python library for accessing 2bit files

  bioinformaticstwobit

  bioinformaticstwobit

  C

  •

  MIT License

  •99 forks in deeptools/py2bit•2121 stars in deeptools/py2bit•00 issues in deeptools/py2bit•00 pull requests in deeptools/py2bit•Updated Apr 21, 2026Apr 21, 2026

• HiCMatrix

  Public
  Python

  •

  GNU General Public License v3.0

  •88 forks in deeptools/HiCMatrix•1313 stars in deeptools/HiCMatrix•00 issues in deeptools/HiCMatrix•11 pull request in deeptools/HiCMatrix•Updated Sep 4, 2025Sep 4, 2025

• github-actions

  Public archive
  Play around with github actions

  JavaScript

  •

  MIT License

  •11 fork in deeptools/github-actions•00 stars in deeptools/github-actions•00 issues in deeptools/github-actions•1212 pull requests in deeptools/github-actions•Updated Aug 16, 2023Aug 16, 2023

• Knight-Ruiz-Matrix-balancing-algorithm

  Public
  C++

  •44 forks in deeptools/Knight-Ruiz-Matrix-balancing-algorithm•1010 stars in deeptools/Knight-Ruiz-Matrix-balancing-algorithm•55 issues in deeptools/Knight-Ruiz-Matrix-balancing-algorithm•11 pull request in deeptools/Knight-Ruiz-Matrix-balancing-algorithm•Updated Apr 13, 2021Apr 13, 2021

• HiCBrowser

  Public
  Simple web browser to visualize HiC tracks

  visualizationdockerbioinformatics+ 5

  visualizationdockerbioinformaticsbrowsergenomicsepigeneticshi-chicexplorer

  JavaScript

  •

  GNU General Public License v2.0

  •55 forks in deeptools/HiCBrowser•1919 stars in deeptools/HiCBrowser•66 issues in deeptools/HiCBrowser•22 pull requests in deeptools/HiCBrowser•Updated Dec 12, 2019Dec 12, 2019

• hicBuildMatrixCpp

  Public
  C++ implementation of hicBuildMatrix

  C++

  •

  MIT License

  •22 forks in deeptools/hicBuildMatrixCpp•22 stars in deeptools/hicBuildMatrixCpp•00 issues in deeptools/hicBuildMatrixCpp•00 pull requests in deeptools/hicBuildMatrixCpp•Updated Oct 16, 2019Oct 16, 2019

• docker-hicbrowser

  Public
  Docker container for easy deployment of the HiCBrowser

  Dockerfile

  •

  GNU General Public License v2.0

  •00 forks in deeptools/docker-hicbrowser•00 stars in deeptools/docker-hicbrowser•00 issues in deeptools/docker-hicbrowser•00 pull requests in deeptools/docker-hicbrowser•Updated Aug 11, 2019Aug 11, 2019

• deeptools_intervals

  Public
  A python library for constructing interval trees with associated exon/annotation information

  bioinformaticsinterval-treegtf+ 1

  bioinformaticsinterval-treegtfbed

  C

  •

  MIT License

  •22 forks in deeptools/deeptools_intervals•77 stars in deeptools/deeptools_intervals•22 issues in deeptools/deeptools_intervals•00 pull requests in deeptools/deeptools_intervals•Updated Aug 7, 2019Aug 7, 2019

• docker-galaxy-hicexplorer

  Public
  Galaxy Docker Image for the HiCExplorer

  HTML

  •

  MIT License

  •33 forks in deeptools/docker-galaxy-hicexplorer•1111 stars in deeptools/docker-galaxy-hicexplorer•33 issues in deeptools/docker-galaxy-hicexplorer•00 pull requests in deeptools/docker-galaxy-hicexplorer•Updated Mar 3, 2019Mar 3, 2019