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.
  ☆14Updated 2 years ago
• zhongmicai / Hic_tools_collection
  ☆12Updated 6 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
• magnitov / pentad
  A simple tool to perform the calculation and visualization of the average chromatin A/B compartment.
  ☆14Updated 2 years ago
• shawnzhangyx / cvdc_scripts
  scripts for analyzing the CVDC data.
  ☆20Updated 6 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…
  ☆26Updated 9 months ago
• junjunlab / GetTransTool
  Extract longest transcript or longest CDS transcript from GTF annotation file or gencode transcripts fasta file.
  ☆21Updated 3 years ago
• deLaatLab / pipe4C
  4C-seq processing pipeline
  ☆26Updated 10 months ago
• yiliao1022 / Pepper3Dgenome
  ☆16Updated 3 years ago
• Tian-Dechao / diffDomain
  DiffDomain is a statistically sound method for detecting differential TADs between conditions
  ☆17Updated 6 months ago
• ma-compbio / Phylo-HMRF
  ☆17Updated 5 years ago
• XiaoTaoWang / domaincaller
  A Python implementation of the original DI domain caller
  ☆12Updated 5 years ago
• kcakdemir / HiCPlotter
  “When everything is connected to everything else, for better or worse, everything matters.” Bruce Mau
  ☆19Updated 5 years ago
• sunyumail93 / PipeRNAseq
  A comprehensive pipeline for RNAseq data analysis
  ☆22Updated last year
• LappalainenLab / lorals_paper_code
  ☆27Updated 3 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
• 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 …
  ☆21Updated last year
• XiaoTaoWang / EagleC
  A deep-learning framework for predicting a full range of structural variations from bulk and single-cell contact maps
  ☆61Updated 4 months ago
• khuang28jhu / bs3
  BS-Seeker3: An Ultra-fast, Versatile Pipeline for Mapping Bisulfite-treated Reads.
  ☆29Updated 6 years ago
• petitmingchang / TO-GCN
  Pipeline of time-ordered gene coexpression network (TO-GCN) construction from three-dimensional (gene expression, condition, and time) da…
  ☆52Updated 2 years ago
• hanlinqian / IntegrativeNetworkMap
  ☆23Updated 3 years ago
• mirnylab / hiclib-legacy
  A legacy repository. Was replaced by distiller, cooler, and cooltools.
  ☆21Updated 5 years ago
• zyndagj / BSMAPz
  Updated and optimized fork of BSMAP
  ☆23Updated 5 years ago
• XiaoTaoWang / HiCPeaks
  A Python implementation for BH-FDR and HiCCUPS
  ☆53Updated 3 weeks ago
• RitchieLabIGH / IRFinder
  ☆22Updated 2 years ago
• dozmorovlab / TADCompare
  Package for analysis and characterization of differential TADs
  ☆26Updated 3 years ago
• dixonlab / hic_breakfinder
  ☆37Updated 6 years ago
• StevenWingett / HiCUP
  Hi-C data processing pipeline
  ☆38Updated last year
• liangfan01 / pipeline-for-isoseq
  ☆14Updated 7 years ago
• YaqiangCao / cLoops2
  Enhanced and elegant flexible peak/loop/domain -calling and analysis tool for 1D/3D genomic data.
  ☆52Updated 7 months ago