hi-c

There are 3 repositories under hi-c topic.

• HiC_tools

  mdozmorov / HiC_tools

  A collection of tools for Hi-C data analysis

  3d-genomehi-cchromatin
  504

• aidenlab / juicer

  A One-Click System for Analyzing Loop-Resolution Hi-C Experiments

  3d-genome3d-genome-browsergenomicshi-cbioinformaticsngs
  Language:Shell 393

• maxplanck-ie / snakepipes

  Customizable workflows based on snakemake and python for the analysis of NGS data

  ngsrna-seqchip-seqworkflowatac-seqhi-cbisulfite-sequencingsnakemake
  Language:Python 372

• higlass / higlass

  Fast, flexible and extensible genome browser.

  genomicsvisualizationhiglasshi-cgehlenborglab
  Language:JavaScript 304

• open2c / cooler

  A cool place to store your Hi-C

  contact-matrixhdf5pythonsparsegenomicshi-cbioinformaticsfile-formatcooler3d-genomechromatinngs
  Language:Python 192

• hms-dbmi / hic-data-analysis-bootcamp

  Workshop on measuring, analyzing, and visualizing the 3D genome with Hi-C data.

  gehlenborglabdata-visualizationhi-chiglasscooler4d-nucleome-networkhipiler
  Language:Jupyter Notebook 187

• mdozmorov / HiC_data

  A (continuously updated) collection of references to Hi-C data. Predominantly human/mouse Hi-C data, with replicates.

  3-dchromatinhi-c
  155
• cLoops

  YaqiangCao / cLoops

  Accurate and flexible loops calling tool for 3D genomic data.

  bioinformaticschia-pethichipchromatin-interaction3d-genomehi-cclusteringdbscanpythonngsalgorithmchromatin-loopspipelinesequencingstripeschromatin-stripesloops-callingtooltrac-loopingexample-data
  Language:Python 108

• 3DGenomes / TADbit

  TADbit is a complete Python library to deal with all steps to analyze, model and explore 3C-based data. With TADbit the user can map FASTQ files to obtain raw interaction binned matrices (Hi-C like matrices), normalize and correct interaction matrices, identify and compare the so-called Topologically Associating Domains (TADs), build 3D models from the interaction matrices, and finally, extract structural properties from the models. TADbit is complemented by TADkit for visualizing 3D models

  pythonchromatinmapping3d-modelshi-cngs
  Language:Python 98

• lh3 / hickit

  TAD calling, phase imputation, 3D modeling and more for diploid single-cell Hi-C (Dip-C) and general Hi-C

  bioinformaticsgenomicshi-c
  Language:C 95

• open2c / pairtools

  flexible suite of CLI tools for contact extraction (.pairs) from sequencing data (Hi-C, Micro-C and other chromosome capture methods)

  3d-genomebioinformaticsfile-formatterhi-cngspythonpairs-file
  Language:Python 89

• zengxiaofei / HapHiC

  HapHiC: a fast, reference-independent, allele-aware scaffolding tool based on Hi-C data

  assemblychromosomegenomehi-cscaffoldinghaplotypephasing3d-dnalachesissalsayahsallhichifiasmpore-c
  Language:Python 85

• 4dn-dcic / pairix

  1D/2D indexing and querying on bgzipped text file with a pair of genomic coordinates

  hi-crandom-accessbgzipbioinformaticscpythonpypairixpairs
  Language:C 83

• open2c / distiller-nf

  A modular Hi-C mapping pipeline

  pipelinenextflowhi-c
  Language:Groovy 80

• nf-core / hic

  Analysis of Chromosome Conformation Capture data (Hi-C)

  nf-corenextflowhi-cchromosome-conformation-captureworkflowpipeline
  Language:Nextflow 76
• coolpuppy

  open2c / coolpuppy

  A versatile tool to perform pile-up analysis on Hi-C data in .cool format.

  hi-cpileupcontact-matrixgenomicssparse-matrixbioinformaticspython
  Language:Python 72

• robinweide / GENOVA

  GENome Organisation Visual Analytics

  tadloophi-ccompartmentsvisualization
  Language:R 63

• 4dn-dcic / hic2cool

  Lightweight converter between hic and cool contact matrices.

  hi-cconvertercoolerjuicercontact-matricesbioinformatics
  Language:Python 60

• koszullab / chromosight

  Computer vision based program for pattern recognition in chromosome (Hi-C) contact maps

  hi-cgenomicschromatin-loopspattern-detection
  Language:Python 59

• XiaoTaoWang / HiCLift

  A fast and efficient tool for converting chromatin interaction data between genome assemblies

  3d-genomehi-cliftover
  Language:Python 59

• tanghaibao / allhic

  Genome scaffolding based on HiC data in heterozygous and high ploidy genomes

  hi-cgenomicsgenome-assemblygolanggenetic-algorithmpolyploidheterozygousgenome-scaffoldinginter-contig-linkscontigspipelinelachesis
  Language:Jupyter Notebook 57

• 4dn-dcic / docker-4dn-hic

  Docker for 4DN Hi-C processing pipeline

  hi-cbioinformaticsdockerpairixcoolerbwajuicerpairsqc
  Language:Common Workflow Language 55
• mustache

  ay-lab / mustache

  Multi-scale Detection of Chromatin Loops from Hi-C and Micro-C Maps using Scale-Space Representation

  chromatin-loopsgenomicshi-cmicro-c
  Language:Python 55

• ay-lab / dcHiC

  dcHiC: Differential compartment analysis for Hi-C datasets

  hi-cbioinformaticsgenomechromatin
  Language:R 54

• tanjimin / C.Origami

  C.Origami, a prediction and screening framework for cell type-specific 3D chromatin structure.

  chromatincomputational-biologyconvolutional-neural-networkdeep-learninggenomicshi-ctransformer
  Language:Python 54

• XiaoTaoWang / NeoLoopFinder

  A computation framework for genome-wide detection of enhancer-hijacking events from chromatin interaction data in re-arranged genomes

  hi-cstructural-variationenhancer-hijacking
  Language:Python 52

• hms-dbmi / 3d-genome-processing-tutorial

  A 3D genome data processing tutorial for ISMB/ECCB 2017

  gehlenborglab4d-nucleome-networkhi-cvisualizationhiglasstutorial
  Language:Jupyter Notebook 48

• XiaoTaoWang / HiC_pipeline

  An easy-to-use Hi-C data processing software supporting distributed computation.

  pythonhi-cpipelinebioinformaticschromosome-conformation-capturecoolerpairs4d-nucleome-networkarima
  Language:Python 48

• open2c / polychrom

  Chromosome polymer simulations and in silico capture experiments

  loop-extrusionsimulationpolymerchromatinchromosomeshi-c
  Language:Python 42

• XiaoTaoWang / HiCPeaks

  A Python implementation for BH-FDR and HiCCUPS

  pythonhi-cchromatinpeaksloopscontact-matrixbioinformaticsgenomicscooler
  Language:Python 39

• XiaoTaoWang / TADLib

  A Library to Explore Chromatin Interaction Patterns for Topologically Associating Domains

  pythonhi-ctadtadsbioinformaticsgenomicschromatincontact-matrixcooler
  Language:Python 39

• koszullab / instaGRAAL

  Large genome reassembly based on Hi-C data, continuation of GRAAL

  genome-assemblygenomics3chi-cscaffolding
  Language:Cuda 38

• YaqiangCao / cLoops2

  Enhanced and elegant flexible peak/loop/domain -calling and analysis tool for 1D/3D genomic data.

  bioinformatics-toolchromatin-interactioncloops2clusteringloopspeaks3d-genome3d-genome-visualizationdomainsstripespythonchia-pethi-ctrac-loopinghichipdifferential-enriched-loopsun-limited-resolutionnext-generation-sequencingrehoboammontage
  Language:Python 38

• koszullab / hicstuff

  Simple library/pipeline to generate and handle Hi-C data.

  hi-c3cgenomicsbioinformaticsbioinformatics-pipeline
  Language:Python 35

• higlass / clodius

  Clodius is a tool for breaking up large data sets into smaller tiles that can subsequently be displayed using an appropriate viewer.

  gehlenborglabhi-chiglass
  Language:Python 34

• QData / ChromeGCN

  Bioinformatics 2020: Graph Neural Networks for DNA Sequence Classification

  graph-neural-networksgenomicsgraph-convolutional-networksdnadna-sequenceshi-c
  Language:Python 31