Alternatives and similar repositories for HiCpipe

Users that are interested in HiCpipe are comparing it to the libraries listed below

• shuzhangcourage / HiC-data-analysis
  General analysis of HiC data, including compartment A/B, domains and loops.
  ☆13Updated 2 years ago
• zhongmicai / Hic_tools_collection
  ☆12Updated 6 years ago
• shawnzhangyx / cvdc_scripts
  scripts for analyzing the CVDC data.
  ☆19Updated 5 years ago
• magnitov / pentad
  A simple tool to perform the calculation and visualization of the average chromatin A/B compartment.
  ☆14Updated 2 years ago
• XiaoTaoWang / domaincaller
  A Python implementation of the original DI domain caller
  ☆12Updated 5 years ago
• CSOgroup / CALDER2
  CALDER is a Hi-C analysis tool that allows: (1) compute chromatin domains from whole chromosome contacts; (2) derive their non-linear hie…
  ☆24Updated 6 months ago
• ma-compbio / Phylo-HMRF
  ☆17Updated 4 years ago
• ahansenlab / RCMC_analysis_code
  Code associated with with the 2023 Nature Genetics Paper "Region Capture Micro-C reveals coalescence of enhancers and promoters into nest…
  ☆12Updated 2 years ago
• LappalainenLab / lorals_paper_code
  ☆27Updated 3 years ago
• XiaoTaoWang / EagleC
  A deep-learning framework for predicting a full range of structural variations from bulk and single-cell contact maps
  ☆61Updated 2 months ago
• WGLab / LIQA
  Long-read Isoform Quantification and Analysis
  ☆38Updated 7 months ago
• kcakdemir / HiCPlotter
  “When everything is connected to everything else, for better or worse, everything matters.” Bruce Mau
  ☆19Updated 5 years ago
• dekkerlab / crane-nature-2015
  code associated with crane-nature-2015, 10.1038/nature14450
  ☆36Updated 10 years ago
• dixonlab / hic_breakfinder
  ☆37Updated 6 years ago
• dekkerlab / cworld-dekker
  perl cworld module and collection of utility/analysis scripts for C data (3C, 4C, 5C, Hi-C)
  ☆67Updated 6 years ago
• yiliao1022 / Pepper3Dgenome
  ☆15Updated 3 years ago
• GuoliangLi-HZAU / ChIA-PET_Tool_V3
  ChIA-PET, HiChIP, PLAC-Seq data analysis, with linker detection, linker filter, or restriction process for HiChIP, mapping, call cluster …
  ☆20Updated last year
• dozmorovlab / TADCompare
  Package for analysis and characterization of differential TADs
  ☆26Updated 3 years ago
• CSOgroup / CALDER
  ☆22Updated 2 years ago
• XiaoTaoWang / HiCPeaks
  A Python implementation for BH-FDR and HiCCUPS
  ☆52Updated 6 months ago
• vaquerizaslab / tadtool
  TADtool is an interactive tool for the identification of meaningful parameters in TAD-calling algorithms for Hi-C data.
  ☆48Updated 2 years ago
• XiaoTaoWang / TADLib
  A Library to Explore Chromatin Interaction Patterns for Topologically Associating Domains
  ☆44Updated 3 years ago
• mirnylab / hiclib-legacy
  A legacy repository. Was replaced by distiller, cooler, and cooltools.
  ☆21Updated 5 years ago
• BlanchetteLab / HIFI
  Hi-C Interaction Frequency Inference (HIFI): High-resolution estimation of DNA-DNA interaction frequency from Hi-C data
  ☆24Updated 3 years ago
• dozmorovlab / multiHiCcompare
  Joint normalization of multiple Hi-C matrices, visualization and detection of differential chromatin interactions, supporting covariates.
  ☆10Updated 3 years ago
• Zhong-Lab-UCSD / HiCtool
  Python library for processing and visualizing Hi-C data
  ☆20Updated 5 years ago
• YaoLab-Bioinfo / shinyChromosome
  an R/Shiny application for interactive creation of non-circular plots of whole genomes
  ☆45Updated 5 months ago
• TcbfGroup / Tcbf
  A pipeline for identifying conserved topologically associating domain boundaries among multiple species.
  ☆16Updated 4 months ago
• zyndagj / BSMAPz
  Updated and optimized fork of BSMAP
  ☆23Updated 4 years ago
• XiaoTaoWang / HiCLift
  A fast and efficient tool for converting chromatin interaction data between genome assemblies
  ☆75Updated 3 months ago