3d-genome

There are 5 repositories under 3d-genome topic.

HiC_tools
mdozmorov / HiC_tools
A collection of tools for Hi-C data analysis
3d-genome hi-c chromatin
503
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 393
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 191
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 107
open2c / pairtools
flexible suite of CLI tools for contact extraction (.pairs) from sequencing data (Hi-C, Micro-C and other chromosome capture methods)
3d-genome bioinformatics file-formatter hi-c ngs python pairs-file
Language:Python 89
ma-compbio / Higashi
single-cell Hi-C, scHi-C, Hi-C, 3D genome, nuclear organization, hypergraph
single-cell hypergraph 3d-genome machine-learning
Language:Jupyter Notebook 70
XiaoTaoWang / HiCLift
A fast and efficient tool for converting chromatin interaction data between genome assemblies
3d-genome hi-c liftover
Language:Python 59
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 38
ma-compbio / SNIPER
nuclear compartments, subcompartments, nuclear organization, Hi-C, autoencoder
3d-genome machine-learning nuclear-compartments
Language:Python 29
ma-compbio / MATCHA
multiway chromatin interaction, 3D genome, single-nucleus, hypergraph representation learning
3d-genome hypergraph machine-learning multiway-interactions hypergraph-learning
Language:Python 28
kundajelab / genomedisco
Software for comparing contact maps from HiC, CaptureC and other 3D genome data.
bioinformatics bioinformatics-pipeline hi-c hic contact-matrix 3d-genome 3c capture-c
Language:Jupyter Notebook 25
ma-compbio / Fast-Higashi
single-cell Hi-C, scHi-C, Hi-C, 3D genome, nuclear organization, tensor decomposition
3d-genome machine-learning single-cell tensor-decomposition
Language:Jupyter Notebook 16
ma-compbio / Phylo-HMRF
3d-genome comparative-genomics gaussian-process machine-learning
Language:Python 15
flekschas / hipiler
Visual exploration of large genome interaction matrices with interactive small multiples.
hi-c visualization genomics small-multiples chromosome-conformation-capture 3d-genome
Language:JavaScript 13
ibn-salem / sevenC
7C: Computational Chromosome Conformation Capture by Correlation of ChIP-seq at CTCF motifs
chip-seq hi-c chromatin-interaction sequence-motif transcription-factors prediction r-package 3d-genome
Language:R 12
ma-compbio / scGHOST
single-cell Hi-C, scHi-C, Hi-C, 3D genome, nuclear organization, genome subcompartment
3d-genome machine-learning single-cell
Language:Jupyter Notebook 12
XiaoTaoWang / Best-Labs-of-3D-Genome
Data and the co-authored network I extracted for lab selection in 3D genome research field
3d-genome hi-c laboratory network
Language:Python 12
gersteinlab / HiC-spector
Spectral and reproducibility analysis of Hi-C contact maps
hi-c 3d-genome
Language:Julia 10
Tian-Dechao / diffDomain
DiffDomain is a statistically sound method for detecting differential TADs between conditions
tads 3d-genome differential hi-c python r
Language:Python 10
ZhangGroup-MITChemistry / DRAGON
3d-genome genomics epigenomics molecular-dynamics chromatin-structure
Language:Python 10
data-fun / 3d-genome-builder
3DGB is a workflow to build 3D models of genomes from HiC data
hic 3d-genome vizualization
Language:Python 9
ma-compbio / GAGE-seq
Data processing and analysis workflow for GAGE-seq, a coassay of single-cell HiC and single-cell RNA-seq
3d-genome epigenomics scrna-seq single-cell schi-c
Language:Jupyter Notebook 8
Genome3d / psychiatric_and_cognitive_multimorbidities
Analysis of regulatory impacts of GWAS SNPs associated with psychiatric disorders and cognitive functioning.
schizophrenia depression hi-c psychiatric-disorders cognition adhd bipolar-disorder 3d-genome gene-regulatory-network anxiety multi-morbidity eqtl
Language:HTML 7
3DGenomes / MethodsMolBiol
tutorial-exercises chromatin-interaction hi-c 3d-genome bioinformatics
Language:Jupyter Notebook 5
ma-compbio / UNADON
Transformer-based model to predict genome-wide chromosome spatial position
3d-genome deep-learning nuclear-architecture transformer tsa-seq
Language:Python 5
cellular-genomics / python-FIREcaller
FIREcaller: Python library for detecting Frequently Interacting REgions (FIREs) from Hi-C data
genomics hic genomic-data-analysis 3d-genome cooler
Language:Python 4
gersteinlab / MrTADFinder
a method to identify TADs in Hi-C data
hi-c 3d-genome
Language:Julia 4
cellular-genomics / cluster-paired-end-tags
Script to cluster Paired End Tags (PETs) from chromatin conformation capture (3C) experiments
genomics 3d-genome genomic-data-analysis
Language:Python 3
flekschas / higlass-fancy
A collection of fancy HiGlass view configs
higlass hi-c 3d-genome fancy
3
Genome3d / alcohol-dependence
Analysis of tissue-specific regulatory impacts of alcohol dependence-associated SNPs.
alcohol-dependence gene-regulatory-network adh-genes hi-c 3d-genome eqtl
Language:HTML 3
OluwadareLab / ParticleChromo3D
Using Particle Swarm Algorithm for chromosome three-dimensional structure construction
3d-genome 3d-reconstruction particle-swarm-optimization oluwadare-lab
Language:Jupyter Notebook 3
OluwadareLab / ParticleChromo3D_Plus
A Web-Server implementation of ParticleChromo3D for 3D chromosome structure reconstruction
3d-genome 3d-reconstruction oluwadare-lab pso-algorithm
Language:Python 3
PavriLab / hicer-nf
Nextflow workflow for basic HiC data processing
next-generation-sequencing nextflow 3d-genome docker hi-c
Language:HTML 3
kuzobuta / hic_paper_NG_2019
Processed data set of Miura et al., Nature Genetics, 2019
bioinformatics hi-c contact-matrices repli-seq 3d-genome genomics
Language:R 2
ma-compbio / SPIN
nuclear compartmentalization, 3D genome, nuclear bodies, MRF
3d-genome markov-random-field genome-compartmentalization genome-segmentation nuclear-compartmentalization nuclear-genome
Language:Python 2
hellosunking / Microcket
Fast and flexiable Hi-C/Micro-C data analyzer
3d-genome
Language:C++ 1

3d-genome

mdozmorov / HiC_tools

aidenlab / juicer

open2c / cooler

YaqiangCao / cLoops

open2c / pairtools

ma-compbio / Higashi

XiaoTaoWang / HiCLift

YaqiangCao / cLoops2

ma-compbio / SNIPER

ma-compbio / MATCHA

kundajelab / genomedisco

ma-compbio / Fast-Higashi

ma-compbio / Phylo-HMRF

flekschas / hipiler

ibn-salem / sevenC

ma-compbio / scGHOST

XiaoTaoWang / Best-Labs-of-3D-Genome

gersteinlab / HiC-spector

Tian-Dechao / diffDomain

ZhangGroup-MITChemistry / DRAGON

data-fun / 3d-genome-builder

ma-compbio / GAGE-seq

Genome3d / psychiatric_and_cognitive_multimorbidities

3DGenomes / MethodsMolBiol

ma-compbio / UNADON

cellular-genomics / python-FIREcaller

gersteinlab / MrTADFinder

cellular-genomics / cluster-paired-end-tags

flekschas / higlass-fancy

Genome3d / alcohol-dependence

OluwadareLab / ParticleChromo3D

OluwadareLab / ParticleChromo3D_Plus

PavriLab / hicer-nf

kuzobuta / hic_paper_NG_2019

ma-compbio / SPIN

hellosunking / Microcket