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
  ☆50Updated 6 years ago
• AndreasHeger / gat
  Genomic Association Tester
  ☆35Updated 2 years ago
• kundajelab / idr
  IDR
  ☆31Updated 2 years ago
• parklab / HiNT
  HiC for copy Number variation and Translocation detection
  ☆40Updated 4 years ago
• vaquerizaslab / tadtool
  TADtool is an interactive tool for the identification of meaningful parameters in TAD-calling algorithms for Hi-C data.
  ☆49Updated 3 years ago
• XiaoTaoWang / TADLib
  A Library to Explore Chromatin Interaction Patterns for Topologically Associating Domains
  ☆45Updated 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
  ☆113Updated 4 years ago
• deLaatLab / pipe4C
  4C-seq processing pipeline
  ☆26Updated 9 months ago
• mortazavilab / swan_vis
  A Python library to visualize and analyze long-read transcriptomes
  ☆64Updated 8 months ago
• ay-lab / dcHiC
  dcHiC: Differential compartment analysis for Hi-C datasets
  ☆73Updated last year
• XiaoTaoWang / HiCPeaks
  A Python implementation for BH-FDR and HiCCUPS
  ☆53Updated this week
• nerettilab / RepEnrich2
  RepEnrich2 is an updated method to estimate repetitive element enrichment using high-throughput sequencing data.
  ☆41Updated 3 years ago
• khuang28jhu / bs3
  BS-Seeker3: An Ultra-fast, Versatile Pipeline for Mapping Bisulfite-treated Reads.
  ☆29Updated 6 years ago
• maxplanck-ie / HiCAssembler
  Software to assemble contigs/scaffolds into chromosomes using Hi-C data
  ☆28Updated last year
• XiaoTaoWang / HiCLift
  A fast and efficient tool for converting chromatin interaction data between genome assemblies
  ☆77Updated 5 months ago
• open2c / coolpuppy
  A versatile tool to perform pile-up analysis on Hi-C data in .cool format.
  ☆80Updated last year
• dekkerlab / crane-nature-2015
  code associated with crane-nature-2015, 10.1038/nature14450
  ☆37Updated 10 years ago
• rjdkmr / gcMapExplorer
  Genome Contact Map Explorer - gcMapExplorer. Visit:
  ☆21Updated 3 years ago
• Magdoll / SQANTI2
  SQANTI2 is now replaced by SQANTI3. Please go to: https://github.com/ConesaLab/SQANTI3
  ☆38Updated 5 years ago
• 4dn-dcic / docker-4dn-hic
  Docker for 4DN Hi-C processing pipeline
  ☆61Updated last year
• tariks / peakachu
  Genome-wide contact analysis using sklearn
  ☆72Updated last year
• XiaoTaoWang / NeoLoopFinder
  A computation framework for genome-wide detection of enhancer-hijacking events from chromatin interaction data in re-arranged genomes
  ☆75Updated 2 years ago
• 4dn-dcic / pairix
  1D/2D indexing and querying on bgzipped text file with a pair of genomic coordinates
  ☆92Updated 11 months ago
• FelixKrueger / SNPsplit
  Allele-specific alignment sorting
  ☆61Updated 2 years ago
• dejunlin / hicrep
  Python implementation of HiCRep stratum-adjusted correlation coefficient of Hi-C data with Cooler sparse contact matrix support
  ☆40Updated last year
• dnaase / Bis-tools
  A collection of tools to deal with Bisulfite-seq/NOMe-seq (SNP/Methylation calling: BisSNP; HMM segmentation: DMNTools; Visualization/Clu…
  ☆32Updated 4 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
• agalitsyna / RedClib
  Red-C data processing
  ☆15Updated 2 years ago
• TaoYang-dev / hicrep
  R package to evaluate the reproducibility of Hi-C data
  ☆26Updated 2 years ago
• ENCODE-DCC / long-read-rna-pipeline
  ENCODE long read RNA-seq pipeline
  ☆52Updated 2 years ago