Alternatives and similar repositories for dcHiC:

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

• open2c / pairtools
  Extract 3D contacts (.pairs) from sequencing alignments
  ☆108Updated last month
• XiaoTaoWang / NeoLoopFinder
  A computation framework for genome-wide detection of enhancer-hijacking events from chromatin interaction data in re-arranged genomes
  ☆62Updated last year
• kundajelab / 3DChromatin_ReplicateQC
  Software to compute reproducibility and quality scores for Hi-C data
  ☆46Updated 5 years ago
• XiaoTaoWang / HiCLift
  A fast and efficient tool for converting chromatin interaction data between genome assemblies
  ☆70Updated last year
• dekkerlab / cworld-dekker
  perl cworld module and collection of utility/analysis scripts for C data (3C, 4C, 5C, Hi-C)
  ☆66Updated 5 years ago
• tariks / peakachu
  Genome-wide contact analysis using sklearn
  ☆64Updated 11 months ago
• yezhengSTAT / CUTTag_tutorial
  Tutorial Website
  ☆57Updated 4 years ago
• ay-lab / fithic
  Fit-Hi-C is a tool for assigning statistical confidence estimates to chromosomal contact maps produced by genome-wide genome architecture…
  ☆82Updated 2 years ago
• 4dn-dcic / hic2cool
  Lightweight converter between hic and cool contact matrices.
  ☆68Updated 8 months ago
• ay-lab / mustache
  Multi-scale Detection of Chromatin Loops from Hi-C and Micro-C Maps using Scale-Space Representation
  ☆69Updated last month
• dejunlin / hicrep
  Python implementation of HiCRep stratum-adjusted correlation coefficient of Hi-C data with Cooler sparse contact matrix support
  ☆37Updated last year
• open2c / quaich
  snakemake pipeline for Hi-C post-processing
  ☆22Updated 8 months ago
• open2c / coolpuppy
  A versatile tool to perform pile-up analysis on Hi-C data in .cool format.
  ☆79Updated 4 months 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…
  ☆19Updated last year
• 4dn-dcic / docker-4dn-hic
  Docker for 4DN Hi-C processing pipeline
  ☆59Updated 3 months ago
• JinLabBioinfo / HiCorr
  HiCorr: a Hi-C data bias-correction pipeline
  ☆28Updated last year
• open2c / distiller-nf
  A modular Hi-C mapping pipeline
  ☆92Updated 3 months ago
• harbourlab / SparK
  Publication quality NGS track plotting
  ☆111Updated 2 years ago
• FelixKrueger / SNPsplit
  Allele-specific alignment sorting
  ☆54Updated 2 years ago
• XiaoTaoWang / TADLib
  A Library to Explore Chromatin Interaction Patterns for Topologically Associating Domains
  ☆40Updated 2 years ago
• tanlongzhi / dip-c
  Tools to analyze Dip-C (or other 3C/Hi-C) data
  ☆64Updated 4 months ago
• dekkerlab / crane-nature-2015
  code associated with crane-nature-2015, 10.1038/nature14450
  ☆34Updated 9 years ago
• LiuLabUB / HMMRATAC
  HMMRATAC peak caller for ATAC-seq data
  ☆100Updated 4 months ago
• XiaoTaoWang / EagleC
  A deep-learning framework for predicting a full range of structural variations from bulk and single-cell contact maps
  ☆58Updated last year
• nerettilab / RepEnrich2
  RepEnrich2 is an updated method to estimate repetitive element enrichment using high-throughput sequencing data.
  ☆38Updated 3 years ago
• vaquerizaslab / chess
  Comparison of Hi-C Experiments using Structural Similarity.
  ☆27Updated last year
• mortazavilab / swan_vis
  A Python library to visualize and analyze long-read transcriptomes
  ☆58Updated last year
• ay-lab / FitHiChIP
  Statistically Significant loops from HiChIP data
  ☆40Updated 11 months ago
• lh3 / hickit
  TAD calling, phase imputation, 3D modeling and more for diploid single-cell Hi-C (Dip-C) and general Hi-C
  ☆109Updated 4 years ago
• open2c / open2c_examples
  ☆17Updated last year