hi-c

There are 5 repositories under hi-c topic.

HiC_tools
mdozmorov / HiC_tools
A collection of tools for Hi-C data analysis
3d-genome hi-c chromatin
619
aidenlab / juicer
A One-Click System for Analyzing Loop-Resolution Hi-C Experiments
3d-genome 3d-genome-browser genomics hi-c bioinformatics ngs
Language:Shell 466
maxplanck-ie / snakepipes
Customizable workflows based on snakemake and python for the analysis of NGS data
ngs rna-seq chip-seq workflow atac-seq hi-c bisulfite-sequencing snakemake
Language:Python 397
higlass / higlass
Fast, flexible and extensible genome browser.
genomics visualization higlass hi-c hidivelab
Language:JavaScript 334
zengxiaofei / HapHiC
HapHiC: a fast, reference-independent, allele-aware scaffolding tool based on Hi-C data
assembly chromosome genome hi-c scaffolding haplotype phasing 3d-dna lachesis salsa yahs allhic hifiasm t2t
Language:Python 238
open2c / cooler
A cool place to store your Hi-C
contact-matrix hdf5 python sparse genomics hi-c bioinformatics file-format cooler 3d-genome chromatin ngs
Language:Python 227
hms-dbmi / hic-data-analysis-bootcamp
Workshop on measuring, analyzing, and visualizing the 3D genome with Hi-C data.
data-visualization hi-c higlass cooler 4d-nucleome-network hipiler hidivelab
Language:Jupyter Notebook 204
mdozmorov / HiC_data
A (continuously updated) collection of references to Hi-C data. Predominantly human/mouse Hi-C data, with replicates.
3-d chromatin hi-c
197
open2c / pairtools
Extract 3D contacts (.pairs) from sequencing alignments
3d-genome bioinformatics file-formatter hi-c ngs python pairs-file
Language:Python 116
lh3 / hickit
TAD calling, phase imputation, 3D modeling and more for diploid single-cell Hi-C (Dip-C) and general Hi-C
bioinformatics genomics hi-c
Language:C 113
cLoops
YaqiangCao / cLoops
Accurate and flexible loops calling tool for 3D genomic data.
bioinformatics chia-pet hichip chromatin-interaction 3d-genome hi-c clustering dbscan python ngs algorithm chromatin-loops pipeline sequencing stripes chromatin-stripes loops-calling tool trac-looping example-data
Language:Python 112
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
python chromatin mapping 3d-models hi-c ngs
Language:Python 106
nf-core / hic
Analysis of Chromosome Conformation Capture data (Hi-C)
nf-core nextflow hi-c chromosome-conformation-capture workflow pipeline
Language:Nextflow 102
open2c / distiller-nf
A modular Hi-C mapping pipeline
pipeline nextflow hi-c
Language:Groovy 100
4dn-dcic / pairix
1D/2D indexing and querying on bgzipped text file with a pair of genomic coordinates
hi-c random-access bgzip bioinformatics c python pypairix pairs u01ca200059 ot2od032119
Language:C 90
robinweide / GENOVA
GENome Organisation Visual Analytics
tad loop hi-c compartments visualization
Language:R 81
tanjimin / C.Origami
C.Origami, a prediction and screening framework for cell type-specific 3D chromatin structure.
chromatin computational-biology convolutional-neural-network deep-learning genomics hi-c transformer
Language:Python 81
coolpuppy
open2c / coolpuppy
A versatile tool to perform pile-up analysis on Hi-C data in .cool format.
hi-c pileup contact-matrix genomics sparse-matrix bioinformatics python
Language:Python 80
mustache
ay-lab / mustache
Multi-scale Detection of Chromatin Loops from Hi-C and Micro-C Maps using Scale-Space Representation
chromatin-loops genomics hi-c micro-c
Language:Python 77
XiaoTaoWang / HiCLift
A fast and efficient tool for converting chromatin interaction data between genome assemblies
3d-genome hi-c liftover
Language:Python 75
4dn-dcic / hic2cool
Lightweight converter between hic and cool contact matrices.
hi-c converter cooler juicer contact-matrices bioinformatics
Language:Python 74
ay-lab / dcHiC
dcHiC: Differential compartment analysis for Hi-C datasets
hi-c bioinformatics genome chromatin
Language:R 73
XiaoTaoWang / NeoLoopFinder
A computation framework for genome-wide detection of enhancer-hijacking events from chromatin interaction data in re-arranged genomes
hi-c structural-variation enhancer-hijacking
Language:Python 73
koszullab / chromosight
Computer vision based program for pattern recognition in chromosome (Hi-C) contact maps
hi-c genomics chromatin-loops pattern-detection
Language:Python 68
wangyibin / CPhasing
C-Phasing/CPhasing: Phasing and scaffolding polyploid genomes based on Pore-C, HiFi-C/CiFi or Hi-C.
genome-assembly haplotype-assembly polyploid pore-c scaffolding phasing ultra-long diploid haplotype-resolved-assembly assembly genome genome-assembler hi-c hic hific hifi-c cifi
Language:Python 66
Jwindler / AutoHiC
A novel genome assembly pipeline based on deep learning
deep-learning genome-assembly hi-c
Language:Python 65
XiaoTaoWang / HiC_pipeline
An easy-to-use Hi-C data processing software supporting distributed computation.
python hi-c pipeline bioinformatics chromosome-conformation-capture cooler pairs 4d-nucleome-network arima
Language:Python 62
4dn-dcic / docker-4dn-hic
Docker for 4DN Hi-C processing pipeline
hi-c bioinformatics docker pairix cooler bwa juicer pairsqc u01ca200059 ot2od032119
Language:Common Workflow Language 60
tanghaibao / allhic
Genome scaffolding based on HiC data in heterozygous and high ploidy genomes
hi-c genomics genome-assembly golang genetic-algorithm polyploid heterozygous genome-scaffolding inter-contig-links contigs pipeline lachesis
Language:Jupyter Notebook 60
open2c / polychrom
Chromosome polymer simulations and in silico capture experiments
loop-extrusion simulation polymer chromatin chromosomes hi-c
Language:Python 52
XiaoTaoWang / HiCPeaks
A Python implementation for BH-FDR and HiCCUPS
python hi-c chromatin peaks loops contact-matrix bioinformatics genomics cooler
Language:Python 52
YaqiangCao / cLoops2
Enhanced and elegant flexible peak/loop/domain -calling and analysis tool for 1D/3D genomic data.
bioinformatics-tool chromatin-interaction cloops2 clustering loops peaks 3d-genome 3d-genome-visualization domains stripes python chia-pet hi-c trac-looping hichip differential-enriched-loops un-limited-resolution next-generation-sequencing rehoboam montage
Language:Python 52
hms-dbmi / 3d-genome-processing-tutorial
A 3D genome data processing tutorial for ISMB/ECCB 2017
4d-nucleome-network hi-c visualization higlass tutorial hidivelab
Language:Jupyter Notebook 51
XiaoTaoWang / TADLib
A Library to Explore Chromatin Interaction Patterns for Topologically Associating Domains
python hi-c tad tads bioinformatics genomics chromatin contact-matrix cooler
Language:Python 44
koszullab / instaGRAAL
Large genome reassembly based on Hi-C data, continuation of GRAAL
genome-assembly genomics 3c hi-c scaffolding
Language:Cuda 42
paulsengroup / hictk
Blazing fast toolkit to work with .hic and .cool files
bioinformatics cli-application conversion cooler cxx cxx-library cxx17 hic hictk hi-c genomics 3d-genomics
Language:C++ 41

hi-c

mdozmorov / HiC_tools

aidenlab / juicer

maxplanck-ie / snakepipes

higlass / higlass

zengxiaofei / HapHiC

open2c / cooler

hms-dbmi / hic-data-analysis-bootcamp

mdozmorov / HiC_data

open2c / pairtools

lh3 / hickit

YaqiangCao / cLoops

3DGenomes / TADbit

nf-core / hic

open2c / distiller-nf

4dn-dcic / pairix

robinweide / GENOVA

tanjimin / C.Origami

open2c / coolpuppy

ay-lab / mustache

XiaoTaoWang / HiCLift

4dn-dcic / hic2cool

ay-lab / dcHiC

XiaoTaoWang / NeoLoopFinder

koszullab / chromosight

wangyibin / CPhasing

Jwindler / AutoHiC

XiaoTaoWang / HiC_pipeline

4dn-dcic / docker-4dn-hic

tanghaibao / allhic

open2c / polychrom

XiaoTaoWang / HiCPeaks

YaqiangCao / cLoops2

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

XiaoTaoWang / TADLib

koszullab / instaGRAAL

paulsengroup / hictk