Alternatives and similar repositories for mHiC:

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

• kundajelab / 3DChromatin_ReplicateQC
  Software to compute reproducibility and quality scores for Hi-C data
  ☆46Updated 5 years ago
• AndreasHeger / gat
  Genomic Association Tester
  ☆30Updated last year
• dekkerlab / crane-nature-2015
  code associated with crane-nature-2015, 10.1038/nature14450
  ☆34Updated 9 years ago
• XiaoTaoWang / TADLib
  A Library to Explore Chromatin Interaction Patterns for Topologically Associating Domains
  ☆40Updated 2 years ago
• vaquerizaslab / tadtool
  TADtool is an interactive tool for the identification of meaningful parameters in TAD-calling algorithms for Hi-C data.
  ☆44Updated 2 years ago
• kundajelab / idr
  IDR
  ☆31Updated 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
• keleslab / mHiC
  ☆12Updated 4 years ago
• deLaatLab / pipe4C
  4C-seq processing pipeline
  ☆23Updated last week
• cmdoret / hicreppy
  Python reimplementation of hicrep with compatibility for sparse matrices
  ☆17Updated 2 years ago
• XiaoTaoWang / NeoLoopFinder
  A computation framework for genome-wide detection of enhancer-hijacking events from chromatin interaction data in re-arranged genomes
  ☆63Updated last year
• nerettilab / RepEnrich2
  RepEnrich2 is an updated method to estimate repetitive element enrichment using high-throughput sequencing data.
  ☆38Updated 3 years ago
• maxplanck-ie / HiCAssembler
  Software to assemble contigs/scaffolds into chromosomes using Hi-C data
  ☆28Updated 6 months ago
• anlin00007 / OnTAD
  An Optimized Nested TAD caller for Hi-C data
  ☆20Updated 3 years ago
• lh3 / hickit
  TAD calling, phase imputation, 3D modeling and more for diploid single-cell Hi-C (Dip-C) and general Hi-C
  ☆108Updated 4 years ago
• dixonlab / hic_breakfinder
  ☆36Updated 5 years ago
• parklab / HiNT
  HiC for copy Number variation and Translocation detection
  ☆37Updated 3 years ago
• NYU-BFX / hic-bench
  A set of pipelines for Hi-C and ChIP-Seq analysis.
  ☆46Updated 11 months ago
• agalitsyna / RedClib
  Red-C data processing
  ☆14Updated last year
• XiaoTaoWang / HiCLift
  A fast and efficient tool for converting chromatin interaction data between genome assemblies
  ☆70Updated last year
• mortazavilab / swan_vis
  A Python library to visualize and analyze long-read transcriptomes
  ☆59Updated last year
• yupenghe / REPTILE
  Predicting regulatory DNA elements based on epigenomic signatures
  ☆28Updated 9 months ago
• tariks / peakachu
  Genome-wide contact analysis using sklearn
  ☆64Updated last year
• Magdoll / SQANTI2
  SQANTI2 is now replaced by SQANTI3. Please go to: https://github.com/ConesaLab/SQANTI3
  ☆38Updated 4 years ago
• ENCODE-DCC / long-read-rna-pipeline
  ENCODE long read RNA-seq pipeline
  ☆45Updated 2 years ago
• XiaoTaoWang / domaincaller
  A Python implementation of the original DI domain caller
  ☆13Updated 4 years ago
• ysora / stripenn
  Architectural stripe detection from 3D genome conformation data
  ☆17Updated last year
• dphansti / mango
  chia pet analysis software
  ☆25Updated 6 years ago
• open2c / quaich
  snakemake pipeline for Hi-C post-processing
  ☆22Updated 9 months ago
• yezhengSTAT / CUTTag_tutorial
  Tutorial Website
  ☆57Updated 4 years ago