Alternatives and similar repositories for docker-4dn-hic

Users that are interested in docker-4dn-hic are comparing it to the libraries listed below

• 4dn-dcic / pairix

  View on GitHub
  1D/2D indexing and querying on bgzipped text file with a pair of genomic coordinates
  ☆92Jan 28, 2025Updated last year
• XiaoTaoWang / HiC_pipeline

  View on GitHub
  An easy-to-use Hi-C data processing software supporting distributed computation.
  ☆62Aug 6, 2024Updated last year
• TaoYang-dev / hicrep

  View on GitHub
  R package to evaluate the reproducibility of Hi-C data
  ☆27Jun 23, 2023Updated 2 years ago
• XiaoTaoWang / TADLib

  View on GitHub
  A Library to Explore Chromatin Interaction Patterns for Topologically Associating Domains
  ☆45Aug 4, 2022Updated 3 years ago
• ay-lab / mustache

  View on GitHub
  Multi-scale Detection of Chromatin Loops from Hi-C and Micro-C Maps using Scale-Space Representation
  ☆79Jan 24, 2025Updated last year
• open2c / coolpuppy

  View on GitHub
  A versatile tool to perform pile-up analysis on Hi-C data in .cool format.
  ☆80Oct 31, 2024Updated last year
• 4dn-dcic / hic2cool

  View on GitHub
  Lightweight converter between hic and cool contact matrices.
  ☆74Jul 15, 2024Updated last year
• XiaoTaoWang / domaincaller

  View on GitHub
  A Python implementation of the original DI domain caller
  ☆12Aug 2, 2020Updated 5 years ago
• open2c / cooler

  View on GitHub
  A cool place to store your Hi-C
  ☆231Jan 28, 2026Updated 2 weeks ago
• kundajelab / 3DChromatin_ReplicateQC

  View on GitHub
  Software to compute reproducibility and quality scores for Hi-C data
  ☆50Apr 12, 2019Updated 6 years ago
• dekkerlab / matrix_paper

  View on GitHub
  Scripts and notebooks used in Akgol Oksuz et al. paper
  ☆11Jan 18, 2021Updated 5 years ago
• dozmorovlab / TADCompare

  View on GitHub
  Package for analysis and characterization of differential TADs
  ☆26Apr 25, 2022Updated 3 years ago
• mdozmorov / HiC_tools

  View on GitHub
  A collection of tools for Hi-C data analysis
  ☆630Jan 31, 2026Updated 2 weeks ago
• hms-dbmi / hic-data-analysis-bootcamp

  View on GitHub
  Workshop on measuring, analyzing, and visualizing the 3D genome with Hi-C data.
  ☆207May 19, 2018Updated 7 years ago
• vaquerizaslab / fanc

  View on GitHub
  FAN-C: Framework for the ANalysis of C-like data
  ☆121Mar 13, 2024Updated last year
• open2c / cooltools

  View on GitHub
  The tools for your .cool's
  ☆160Jul 7, 2025Updated 7 months ago
• agalitsyna / fontanka

  View on GitHub
  Fontanka is a set of tools to work with fountains in Hi-C data. It aims to provide a flexible Python API and specialized CLI for calling …
  ☆12Dec 22, 2025Updated last month
• nanoporetech / pore-c

  View on GitHub
  Pore-C support
  ☆54Feb 22, 2023Updated 2 years ago
• dejunlin / hicrep

  View on GitHub
  Python implementation of HiCRep stratum-adjusted correlation coefficient of Hi-C data with Cooler sparse contact matrix support
  ☆41Jan 31, 2024Updated 2 years ago
• tariks / peakachu

  View on GitHub
  Genome-wide contact analysis using sklearn
  ☆72Mar 23, 2024Updated last year
• dekkerlab / cworld-dekker

  View on GitHub
  perl cworld module and collection of utility/analysis scripts for C data (3C, 4C, 5C, Hi-C)
  ☆67Jun 7, 2019Updated 6 years ago
• ChenFengling / HiCpipe

  View on GitHub
  an efficient Hi-C data processing pipeline
  ☆17Mar 26, 2024Updated last year
• lidaof / g3d

  View on GitHub
  Genomics 3D Visualizer
  ☆14Jun 14, 2024Updated last year
• open2c / pairtools

  View on GitHub
  Extract 3D contacts (.pairs) from sequencing alignments
  ☆125Feb 3, 2026Updated last week
• XiaoTaoWang / HiCPeaks

  View on GitHub
  A Python implementation for BH-FDR and HiCCUPS
  ☆53Dec 29, 2025Updated last month
• CSOgroup / CALDER2

  View on GitHub
  CALDER is a Hi-C analysis tool that allows: (1) compute chromatin domains from whole chromosome contacts; (2) derive their non-linear hie…
  ☆26Apr 16, 2025Updated 9 months ago
• anlin00007 / OnTAD

  View on GitHub
  An Optimized Nested TAD caller for Hi-C data
  ☆25Jun 30, 2021Updated 4 years ago
• PouletAxel / SIP

  View on GitHub
  SIP: Significant Interaction Peak caller
  ☆15Apr 24, 2025Updated 9 months ago
• ryought / hic_hiker

  View on GitHub
  HiC-Hiker: A probabilistic model to determine contig orientation in chromosome-length scaffolds with Hi-C
  ☆26Jan 14, 2021Updated 5 years ago
• ma-compbio / Phylo-HMRF

  View on GitHub
  ☆17Nov 9, 2020Updated 5 years ago
• linguoliang / puzzle-hi-c

  View on GitHub
  ☆16Dec 25, 2024Updated last year
• TcbfGroup / Tcbf

  View on GitHub
  A pipeline for identifying conserved topologically associating domain boundaries among multiple species.
  ☆16Jun 17, 2025Updated 7 months ago
• open2c / cooler-binder

  View on GitHub
  Cooler demo using a Jupyter notebook Binder
  ☆18Sep 24, 2020Updated 5 years ago
• aidenlab / EigenVector

  View on GitHub
  R functions for very fast eigenvector calculation
  ☆11Jan 18, 2023Updated 3 years ago
• agalitsyna / avTAD

  View on GitHub
  Plotting average TAD heatmap for Hi-C data (give TAD segmentation and cool/hiclib interactions map).
  ☆10Jun 5, 2021Updated 4 years ago
• stjude / ChIPseqSpikeInFree

  View on GitHub
  A Spike-in Free ChIP-Seq Normalization Approach for Detecting Global Changes in Histone Modifications
  ☆41Feb 22, 2022Updated 3 years ago
• XiaoTaoWang / EagleC

  View on GitHub
  A deep-learning framework for predicting a full range of structural variations from bulk and single-cell contact maps
  ☆61Aug 28, 2025Updated 5 months ago
• shawnzhangyx / cvdc_scripts

  View on GitHub
  scripts for analyzing the CVDC data.
  ☆20Dec 5, 2019Updated 6 years ago
• mirnylab / hiclib-legacy

  View on GitHub
  A legacy repository. Was replaced by distiller, cooler, and cooltools.
  ☆21Mar 4, 2020Updated 5 years ago