hi-c

There are 165 repositories under hi-c topic.

  • HiC_tools

    mdozmorov/HiC_tools

    A collection of tools for Hi-C data analysis

    559386125

  • aidenlab/juicer

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

    Language:Shell42217315183

  • maxplanck-ie/snakepipes

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

    Language:Python3892048087

  • higlass/higlass

    Fast, flexible and extensible genome browser.

    Language:JavaScript3152357952

  • open2c/cooler

    A cool place to store your Hi-C

    Language:Python2101429852

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

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

    Language:Jupyter Notebook19326249

  • mdozmorov/HiC_data

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

    17813230

  • zengxiaofei/HapHiC

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

    Language:Python1554969
  • cLoops

    YaqiangCao/cLoops

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

    Language:Python109152917

  • lh3/hickit

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

    Language:C10883611

  • open2c/pairtools

    Extract 3D contacts (.pairs) from sequencing alignments

    Language:Python1061116132

  • 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

    Language:Python1001725461

  • nf-core/hic

    Analysis of Chromosome Conformation Capture data (Hi-C)

    Language:Nextflow931409656

  • open2c/distiller-nf

    A modular Hi-C mapping pipeline

    Language:Groovy881014925

  • 4dn-dcic/pairix

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

    Language:C8791914
  • coolpuppy

    open2c/coolpuppy

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

    Language:Python78611212

  • robinweide/GENOVA

    GENome Organisation Visual Analytics

    Language:R72528715

  • XiaoTaoWang/HiCLift

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

    Language:Python693185

  • tanjimin/C.Origami

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

    Language:Python684279

  • 4dn-dcic/hic2cool

    Lightweight converter between hic and cool contact matrices.

    Language:Python6710417

  • ay-lab/dcHiC

    dcHiC: Differential compartment analysis for Hi-C datasets

    Language:R6459710
  • mustache

    ay-lab/mustache

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

    Language:Python6456611

  • koszullab/chromosight

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

    Language:Python6314449

  • Jwindler/AutoHiC

    A novel genome assembly pipeline based on deep learning

    Language:Python594485

  • tanghaibao/allhic

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

    Language:Jupyter Notebook595014

  • XiaoTaoWang/NeoLoopFinder

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

    Language:Python5926816

  • 4dn-dcic/docker-4dn-hic

    Docker for 4DN Hi-C processing pipeline

    Language:Common Workflow Language588418

  • XiaoTaoWang/HiC_pipeline

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

    Language:Python5561620

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

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

    Language:Jupyter Notebook5014010

  • open2c/polychrom

    Chromosome polymer simulations and in silico capture experiments

    Language:Python4792116

  • YaqiangCao/cLoops2

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

    Language:Python453137

  • XiaoTaoWang/HiCPeaks

    A Python implementation for BH-FDR and HiCCUPS

    Language:Python43299

  • koszullab/instaGRAAL

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

    Language:Cuda408459

  • XiaoTaoWang/TADLib

    A Library to Explore Chromatin Interaction Patterns for Topologically Associating Domains

    Language:Python4032711

  • higlass/clodius

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

    Language:Python39145721

  • koszullab/hicstuff

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

    Language:Python368717