hellosunking/Microcket

Fast and flexiable Hi-C/Micro-C data analyzer

Language: C++ - Size: 60.8 MB - Last synced at: 3 days ago - Pushed at: 3 days ago - Stars: 7 - Forks: 0

mdozmorov/HiC_tools

A collection of tools for Hi-C data analysis

Size: 2.81 MB - Last synced at: 9 days ago - Pushed at: 9 days ago - Stars: 586 - Forks: 133

jasonwong-lab/gghic

gghic

Language: R - Size: 40.1 MB - Last synced at: 13 days ago - Pushed at: 13 days ago - Stars: 5 - Forks: 0

sshen82/BandNorm

Simple Normalization Method for single-cell Hi-C

Language: R - Size: 17.8 MB - Last synced at: 16 days ago - Pushed at: 16 days ago - Stars: 1 - Forks: 3

YaqiangCao/cLoops2

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

Language: Python - Size: 251 MB - Last synced at: 15 days ago - Pushed at: 3 months ago - Stars: 47 - Forks: 8

OluwadareLab/ParticleChromo3D

Using Particle Swarm Algorithm for chromosome three-dimensional structure construction

Language: Jupyter Notebook - Size: 143 MB - Last synced at: 27 days ago - Pushed at: 27 days ago - Stars: 4 - Forks: 5

open2c/pairtools

Extract 3D contacts (.pairs) from sequencing alignments

Language: Python - Size: 3.36 MB - Last synced at: 9 days ago - Pushed at: 4 months ago - Stars: 112 - Forks: 34

open2c/cooler

A cool place to store your Hi-C

Language: Python - Size: 88.1 MB - Last synced at: 3 days ago - Pushed at: 6 days ago - Stars: 216 - Forks: 56

aidenlab/juicer

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

Language: Shell - Size: 77.3 MB - Last synced at: about 1 month ago - Pushed at: 6 months ago - Stars: 439 - Forks: 185

OluwadareLab/ParticleChromo3D_Plus

A Web-Server implementation of ParticleChromo3D for 3D chromosome structure reconstruction

Language: Python - Size: 3.04 MB - Last synced at: 3 days ago - Pushed at: about 1 month ago - Stars: 3 - Forks: 2

nf-core/sammyseq

Pipeline for Sequential Analysis of MacroMolecules accessibilitY sequencing (SAMMY-seq) data, to analyze chromatin state.

Language: Nextflow - Size: 2.94 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 4 - Forks: 15

XiaoTaoWang/HiCLift

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

Language: Python - Size: 30.5 MB - Last synced at: about 1 month ago - Pushed at: almost 2 years ago - Stars: 71 - Forks: 5

Tian-Dechao/diffDomain

DiffDomain is a statistically sound method for detecting differential TADs between conditions

Language: Python - Size: 11.1 MB - Last synced at: about 2 months ago - Pushed at: 8 months ago - Stars: 18 - Forks: 4

data-fun/3d-genome-builder

3DGB is a workflow to build 3D models of genomes from HiC data

Language: Python - Size: 32.5 MB - Last synced at: about 2 months ago - Pushed at: 3 months ago - Stars: 14 - Forks: 3

PavriLab/hicer-nf

Nextflow workflow for basic HiC data processing

Language: HTML - Size: 85.3 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 4 - Forks: 1

gersteinlab/HiC-spector

Spectral and reproducibility analysis of Hi-C contact maps

Language: Julia - Size: 48.8 KB - Last synced at: 3 months ago - Pushed at: about 4 years ago - Stars: 12 - Forks: 7

ma-compbio/Higashi

single-cell Hi-C, scHi-C, Hi-C, 3D genome, nuclear organization, hypergraph

Language: Jupyter Notebook - Size: 206 MB - Last synced at: 7 months ago - Pushed at: 8 months ago - Stars: 78 - Forks: 11

ma-compbio/GAGE-seq

Data processing and analysis workflow for GAGE-seq, a coassay of single-cell HiC and single-cell RNA-seq

Language: Jupyter Notebook - Size: 17.4 MB - Last synced at: 7 months ago - Pushed at: about 1 year ago - Stars: 11 - Forks: 0

ma-compbio/scGHOST

single-cell Hi-C, scHi-C, Hi-C, 3D genome, nuclear organization, genome subcompartment

Language: Jupyter Notebook - Size: 2.7 MB - Last synced at: 7 months ago - Pushed at: about 1 year ago - Stars: 18 - Forks: 2

cellular-genomics/python-FIREcaller

FIREcaller: Python library for detecting Frequently Interacting REgions (FIREs) from Hi-C data

Language: Python - Size: 21.5 KB - Last synced at: 6 days ago - Pushed at: about 3 years ago - Stars: 5 - Forks: 1

ma-compbio/Fast-Higashi

single-cell Hi-C, scHi-C, Hi-C, 3D genome, nuclear organization, tensor decomposition

Language: Jupyter Notebook - Size: 1.12 MB - Last synced at: 7 months ago - Pushed at: over 1 year ago - Stars: 17 - Forks: 5

ma-compbio/MATCHA

multiway chromatin interaction, 3D genome, single-nucleus, hypergraph representation learning

Language: Python - Size: 47 MB - Last synced at: 7 months ago - Pushed at: almost 3 years ago - Stars: 29 - Forks: 5

ma-compbio/SNIPER

nuclear compartments, subcompartments, nuclear organization, Hi-C, autoencoder

Language: Python - Size: 2.27 MB - Last synced at: 11 months ago - Pushed at: 11 months ago - Stars: 29 - Forks: 11

jlchen5/Hi-C-Data-analysis

Language: Shell - Size: 7.81 KB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0

ibn-salem/sevenC

7C: Computational Chromosome Conformation Capture by Correlation of ChIP-seq at CTCF motifs

Language: R - Size: 26.8 MB - Last synced at: 23 days ago - Pushed at: over 6 years ago - Stars: 12 - Forks: 2

nucleosome-dynamics/nucleosome_dynamics_MuGVRE

Nucleosome Dynamics wrappers for MuGVRE platform

Language: Python - Size: 96.8 MB - Last synced at: over 1 year ago - Pushed at: about 6 years ago - Stars: 0 - Forks: 0

ma-compbio/Phylo-HMRF

Language: Python - Size: 9.11 MB - Last synced at: over 1 year ago - Pushed at: over 4 years ago - Stars: 15 - Forks: 3

YaqiangCao/cLoops

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

Language: Python - Size: 464 MB - Last synced at: over 1 year ago - Pushed at: about 3 years ago - Stars: 103 - Forks: 48

shuzhenkuang/DeepLncCTCF

DeepLncCTCF for identification and analysis of consensus RNA motifs binding to the genome regulator CTCF

Language: Python - Size: 123 MB - Last synced at: over 1 year ago - Pushed at: almost 5 years ago - Stars: 0 - Forks: 0

shuzhenkuang/DeepCTCFLoop

Deep Learning of Sequence Patterns for CTCF-Mediated Chromatin Loop Formation

Language: Python - Size: 36.1 MB - Last synced at: over 1 year ago - Pushed at: almost 5 years ago - Stars: 1 - Forks: 0

tanlabcode/IM-PET

Language: HTML - Size: 51.7 MB - Last synced at: over 1 year ago - Pushed at: about 6 years ago - Stars: 0 - Forks: 0

cellular-genomics/cluster-paired-end-tags

Script to cluster Paired End Tags (PETs) from chromatin conformation capture (3C) experiments

Language: Python - Size: 251 KB - Last synced at: over 1 year ago - Pushed at: over 4 years ago - Stars: 3 - Forks: 1

flekschas/hipiler

Visual exploration of large genome interaction matrices with interactive small multiples.

Language: JavaScript - Size: 11.9 MB - Last synced at: 20 days ago - Pushed at: over 3 years ago - Stars: 13 - Forks: 0

3DGenomes/MethodsMolBiol

Language: Jupyter Notebook - Size: 43.3 MB - Last synced at: 10 months ago - Pushed at: about 6 years ago - Stars: 5 - Forks: 1

Genome3d/alcohol-dependence

Analysis of tissue-specific regulatory impacts of alcohol dependence-associated SNPs.

Language: HTML - Size: 3.91 MB - Last synced at: over 1 year ago - Pushed at: over 2 years ago - Stars: 1 - Forks: 2

Genome3d/psychiatric_and_cognitive_multimorbidities

Analysis of regulatory impacts of GWAS SNPs associated with psychiatric disorders and cognitive functioning.

Language: HTML - Size: 35.3 MB - Last synced at: over 1 year ago - Pushed at: over 2 years ago - Stars: 5 - Forks: 3

dawnmy/HAPPY

Hi-C data Analysis and Processing PIpeline

Language: Python - Size: 38.1 KB - Last synced at: almost 2 years ago - Pushed at: almost 6 years ago - Stars: 0 - Forks: 0

ZhangGroup-MITChemistry/DRAGON

Language: Python - Size: 86.1 MB - Last synced at: almost 2 years ago - Pushed at: almost 2 years ago - Stars: 9 - Forks: 1

ma-compbio/UNADON

Transformer-based model to predict genome-wide chromosome spatial position

Language: Python - Size: 4.73 MB - Last synced at: about 2 years ago - Pushed at: about 2 years ago - Stars: 2 - Forks: 0

kundajelab/genomedisco

Software for comparing contact maps from HiC, CaptureC and other 3D genome data.

Language: Jupyter Notebook - Size: 431 MB - Last synced at: 7 months ago - Pushed at: about 7 years ago - Stars: 25 - Forks: 10

flekschas/higlass-fancy

A collection of fancy HiGlass view configs

Size: 1.37 MB - Last synced at: 3 months ago - Pushed at: over 5 years ago - Stars: 3 - Forks: 0

ma-compbio/SPIN

nuclear compartmentalization, 3D genome, nuclear bodies, MRF

Language: Python - Size: 488 KB - Last synced at: 7 months ago - Pushed at: over 4 years ago - Stars: 2 - Forks: 1

OluwadareLab/CBCR

CBCR: A Curriculum Based Strategy For Chromosome Reconstruction

Language: MATLAB - Size: 1010 KB - Last synced at: about 2 years ago - Pushed at: about 4 years ago - Stars: 0 - Forks: 0

OluwadareLab/ChromeBat

ChromeBat: A Bio-Inspired Approach to 3D Genome Reconstruction

Language: Python - Size: 4.62 MB - Last synced at: about 2 years ago - Pushed at: almost 4 years ago - Stars: 0 - Forks: 0

Genome3d/multimorbidity-atlas

Pipeline to investigate multimorbidity of complex traits/phenotypes by integrating chromatin interaction and expression quantitative trait loci data.

Language: HTML - Size: 25.5 MB - Last synced at: about 2 years ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 1

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

Data and the co-authored network I extracted for lab selection in 3D genome research field

Language: Python - Size: 39.2 MB - Last synced at: over 2 years ago - Pushed at: over 3 years ago - Stars: 10 - Forks: 3

kuzobuta/hic_paper_NG_2019

Processed data set of Miura et al., Nature Genetics, 2019

Language: R - Size: 193 MB - Last synced at: about 2 years ago - Pushed at: almost 4 years ago - Stars: 2 - Forks: 3

LupienLab/3d-reorganization-prostate-cancer

Code, analysis, and results for Hawley, Zhou, et al., Cancer Research, 2021.

Language: HTML - Size: 3.21 GB - Last synced at: over 1 year ago - Pushed at: about 2 years ago - Stars: 0 - Forks: 0

gersteinlab/MrTADFinder

a method to identify TADs in Hi-C data

Language: Julia - Size: 394 KB - Last synced at: about 3 hours ago - Pushed at: about 5 years ago - Stars: 4 - Forks: 3

Genome3d/blood-metabolites-regulation

Language: Python - Size: 14.2 MB - Last synced at: about 2 years ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 1

tanlabcode/rGMAP Fork of wbaopaul/rGMAP

Language: R - Size: 36.2 MB - Last synced at: about 2 years ago - Pushed at: over 6 years ago - Stars: 0 - Forks: 0