amarinderthind/CTCF_Cancer_study

Scripts and workflows for the analysis of CTCF binding site mutations, focusing on their impact on gene regulation and cancer progression.

Language: R - Size: 6.42 MB - Last synced at: about 23 hours ago - Pushed at: 1 day ago - Stars: 0 - Forks: 0

open2c/cooler

A cool place to store your Hi-C

Language: Python - Size: 88.1 MB - Last synced at: 1 day ago - Pushed at: 1 day ago - Stars: 217 - Forks: 56

open2c/distiller-sm

a Snakemake version of distiller - the Open2C Hi-C mapping workflow

Language: Python - Size: 134 KB - Last synced at: 2 days ago - Pushed at: 2 days ago - Stars: 4 - Forks: 3

higlass/higlass

Fast, flexible and extensible genome browser.

Language: JavaScript - Size: 154 MB - Last synced at: 3 days ago - Pushed at: 3 days ago - Stars: 326 - Forks: 52

open2c/pairtools

Extract 3D contacts (.pairs) from sequencing alignments

Language: Python - Size: 3.05 MB - Last synced at: 6 days ago - Pushed at: 6 days ago - Stars: 113 - Forks: 34

munch-group/hic-compartment-borders

Inference of compartment borders using pymc

Language: HTML - Size: 133 MB - Last synced at: 6 days ago - Pushed at: 6 days ago - Stars: 0 - Forks: 0

koszullab/metaTOR

Metagenomic binning based on Hi-C data

Language: Python - Size: 157 MB - Last synced at: 7 days ago - Pushed at: 7 days ago - Stars: 26 - Forks: 9

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: 6 days ago - Pushed at: 8 days ago - Stars: 47 - Forks: 8

wangyibin/CPhasing

C-Phasing/CPhasing: Phasing and scaffolding polyploid genomes based on Pore-C, HiFi-C/CiFi or Hi-C.

Language: Python - Size: 70.5 MB - Last synced at: 9 days ago - Pushed at: 9 days ago - Stars: 37 - Forks: 4

anyuzx/HIPPS-DIMES

Maximum Entropy Based HI-C/Distance Map - Polymer Physics - Structures Method

Language: Jupyter Notebook - Size: 15.5 MB - Last synced at: 14 days ago - Pushed at: 14 days ago - Stars: 13 - Forks: 5

paulsengroup/hictk

Blazing fast toolkit to work with .hic and .cool files

Language: C++ - Size: 10.2 MB - Last synced at: 12 days ago - Pushed at: 12 days ago - Stars: 31 - Forks: 1

Noble-Lab/HiCFoundation

HiCFoundation is a generalizable Hi-C foundation model for chromatin architecture, single-cell and multi-omics analysis across species.

Language: Python - Size: 42.9 MB - Last synced at: 18 days ago - Pushed at: 18 days ago - Stars: 16 - Forks: 3

4dn-dcic/pairix

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

Language: C - Size: 318 MB - Last synced at: 16 days ago - Pushed at: 5 months ago - Stars: 90 - Forks: 14

Plant-Food-Research-Open/assemblyqc

A Nextflow pipeline for evaluating assembly quality

Language: Nextflow - Size: 64.1 MB - Last synced at: about 12 hours ago - Pushed at: about 12 hours ago - Stars: 34 - Forks: 7

XiaoTaoWang/HiCPeaks

A Python implementation for BH-FDR and HiCCUPS

Language: Python - Size: 5.31 MB - Last synced at: 2 days ago - Pushed at: 2 months ago - Stars: 49 - Forks: 10

kevinbdsouza/GraphTransHiC

A Graph Transformer that creates hierarchal representations of HiC.

Language: Python - Size: 7.23 MB - Last synced at: 20 days ago - Pushed at: 21 days ago - Stars: 1 - Forks: 0

sebgra/hicberg

Statistical profiling based program for contact (Hi-C) and pair ended genomic data reconstruction

Language: Python - Size: 148 MB - Last synced at: 11 days ago - Pushed at: 11 days ago - Stars: 1 - Forks: 1

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: 14 days ago - Pushed at: over 6 years ago - Stars: 13 - Forks: 2

SLUR-m-Py/SLURPY

SLUR(M)-py: A SLURM Powered Pythonic Pipeline for Parallel Processing of 3D (Epi)genomic Profiles

Language: Python - Size: 473 KB - Last synced at: 25 days ago - Pushed at: 25 days ago - Stars: 1 - Forks: 0

XiaoTaoWang/HiCLift

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

Language: Python - Size: 30.5 MB - Last synced at: 23 days ago - Pushed at: about 2 years ago - Stars: 73 - Forks: 5

XiaoTaoWang/TADLib

A Library to Explore Chromatin Interaction Patterns for Topologically Associating Domains

Language: Python - Size: 11.1 MB - Last synced at: 20 days ago - Pushed at: almost 3 years ago - Stars: 43 - Forks: 11

ay-lab/mustache

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

Language: Python - Size: 8.76 MB - Last synced at: 13 days ago - Pushed at: 5 months ago - Stars: 74 - Forks: 11

paulsengroup/hictkpy

Python bindings for hictk: read and write .cool and .hic files directly from Python

Language: C++ - Size: 31.9 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 15 - Forks: 0

mdozmorov/HiC_tools

A collection of tools for Hi-C data analysis

Size: 2.81 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 586 - Forks: 133

zengxiaofei/HapHiC

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

Language: Python - Size: 42 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 192 - Forks: 8

paulsengroup/StripePy

StripePy recognizes architectural stripes in 3C and Hi-C contact maps using geometric reasoning

Language: Python - Size: 1.31 MB - Last synced at: 5 days ago - Pushed at: 8 days ago - Stars: 6 - Forks: 3

Ashley-Milton/OAN-epigenetic-profiling

Language: R - Size: 44.9 KB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 0 - Forks: 0

cmdoret/hicreppy

Python reimplementation of hicrep with compatibility for sparse matrices

Language: Python - Size: 219 KB - Last synced at: 9 days ago - Pushed at: over 2 years ago - Stars: 18 - Forks: 2

sshen82/BandNorm

Simple Normalization Method for single-cell Hi-C

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

XiaoTaoWang/NeoLoopFinder

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

Language: Python - Size: 59.8 MB - Last synced at: about 1 month ago - Pushed at: over 1 year ago - Stars: 65 - Forks: 15

XiaoTaoWang/HiC_pipeline

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

Language: Python - Size: 34.6 MB - Last synced at: 30 days ago - Pushed at: 11 months ago - Stars: 58 - Forks: 21

open2c/coolpuppy

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

Language: Python - Size: 109 MB - Last synced at: about 1 month ago - Pushed at: 8 months ago - Stars: 80 - Forks: 12

maxplanck-ie/snakepipes

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

Language: Python - Size: 154 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 395 - Forks: 87

4dn-dcic/hic2cool

Lightweight converter between hic and cool contact matrices.

Language: Python - Size: 142 MB - Last synced at: 7 days ago - Pushed at: 11 months ago - Stars: 73 - Forks: 8

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: Python - Size: 26.9 MB - Last synced at: about 1 month ago - Pushed at: about 2 months ago - Stars: 39 - Forks: 21

tanjimin/C.Origami

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

Language: Python - Size: 242 KB - Last synced at: 10 days ago - Pushed at: 12 months ago - Stars: 75 - Forks: 10

lh3/hickit

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

Language: C - Size: 4.5 MB - Last synced at: about 2 months ago - Pushed at: over 4 years ago - Stars: 107 - Forks: 11

open2c/distiller-nf

A modular Hi-C mapping pipeline

Language: Groovy - Size: 1.33 MB - Last synced at: 24 days ago - Pushed at: 7 months ago - Stars: 94 - Forks: 25

aidenlab/juicer

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

Language: Shell - Size: 77.3 MB - Last synced at: about 2 months ago - Pushed at: 7 months ago - Stars: 439 - Forks: 185

open2c/polychrom

Chromosome polymer simulations and in silico capture experiments

Language: Python - Size: 19.7 MB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 48 - Forks: 16

koszullab/instaGRAAL

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

Language: Cuda - Size: 38.3 MB - Last synced at: 12 days ago - Pushed at: over 1 year ago - Stars: 41 - Forks: 9

seqyuan/trackc

trackc aims to produce beautiful genome tracks that are highly customizable

Language: Python - Size: 49.4 MB - Last synced at: 8 days ago - Pushed at: 2 months ago - Stars: 14 - Forks: 0

tanaylab/shaman

The shaman package - sampling HiC contact matrices for a-parametric normalization

Language: R - Size: 2.22 MB - Last synced at: 16 days ago - Pushed at: over 3 years ago - Stars: 6 - Forks: 1

Tian-Dechao/diffDomain

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

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

tanghaibao/allhic

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

Language: Jupyter Notebook - Size: 30 MB - Last synced at: about 1 month ago - Pushed at: 6 months ago - Stars: 60 - Forks: 14

OpenOmics/HiIP

An awesome Hi-C + ChIP (HiChIP) sequencing pipeline.

Language: Python - Size: 577 KB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 0 - Forks: 0

dyxstat/MetaCC

MetaCC allows scalable and integrative analyses of both long-read and short-read metagenomic Hi-C data

Language: C - Size: 13 MB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 8 - Forks: 2

joachimwolff/scHiCExplorer

Single-cell Hi-C data analysis toolbox

Language: Python - Size: 39.2 MB - Last synced at: 3 months ago - Pushed at: almost 4 years ago - Stars: 26 - Forks: 2

sebastian-gregoricchio/snHiC

Snakemake pipeline for analysis and normalization of Hi-C data starting from fastq.gz files. It includes the possibility to perform grouped analyses, TAD, loops and stripes detections, as well as differential compartment and chromatin interaction analyses.

Language: Python - Size: 5.73 MB - Last synced at: 2 months ago - Pushed at: 4 months ago - Stars: 4 - Forks: 0

mdozmorov/HiC_data

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

Size: 349 KB - Last synced at: 4 months ago - Pushed at: 5 months ago - Stars: 182 - Forks: 30

PavriLab/hicer-nf

Nextflow workflow for basic HiC data processing

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

koszullab/hicstuff Fork of baudrly/hicstuff

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

Language: Python - Size: 10.9 MB - Last synced at: 21 days ago - Pushed at: 7 months ago - Stars: 37 - Forks: 7

Gabrielstav/HiEdge

Configurable Hi-C pipeline that is easy to use

Language: Python - Size: 328 KB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 3 - Forks: 1

zwang-bioinformatics/scHiGex

This repository includes code and a pre-trained model of scHiGex for single-cell gene expression prediction.

Language: Python - Size: 40 MB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 2 - Forks: 0

paulsengroup/hictkR

R bindings for hictk: read .cool and .hic files directly from R

Language: C++ - Size: 11.3 MB - Last synced at: 29 days ago - Pushed at: 29 days ago - Stars: 4 - Forks: 0

nf-core/hic

Analysis of Chromosome Conformation Capture data (Hi-C)

Language: Nextflow - Size: 3.6 MB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 95 - Forks: 57

robinweide/GENOVA

GENome Organisation Visual Analytics

Language: R - Size: 493 MB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 72 - Forks: 15

sa501428/clear-tools

Chromatin Landscape Exploration, Analysis, and Research Tools

Language: Java - Size: 80.9 MB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 2 - Forks: 2

dyxstat/ViralCC

ViralCC: leveraging metagenomic proximity-ligation to retrieve complete viral genomes

Language: Python - Size: 281 KB - Last synced at: 3 months ago - Pushed at: over 1 year ago - Stars: 16 - Forks: 3

GuangyWang/TADsplimer

TADsplimer

Language: Python - Size: 791 KB - Last synced at: 4 months ago - Pushed at: about 4 years ago - Stars: 7 - Forks: 4

lpryszcz/HiCembler

Assembler for HiC data

Language: Python - Size: 156 KB - Last synced at: 9 days ago - Pushed at: over 6 years ago - Stars: 5 - Forks: 0

XiaoTaoWang/StripeCaller

A toolkit for analyzing architectural stripes

Language: Python - Size: 43.9 KB - Last synced at: 7 months ago - Pushed at: 7 months ago - Stars: 19 - Forks: 2

koszullab/chromosight

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

Language: Python - Size: 54.6 MB - Last synced at: 4 months ago - Pushed at: over 2 years ago - Stars: 63 - Forks: 9

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: over 4 years ago - Stars: 12 - Forks: 7

QData/ChromeGCN

Bioinformatics 2020: Graph Neural Networks for DNA Sequence Classification

Language: Python - Size: 427 KB - Last synced at: about 2 months ago - Pushed at: over 4 years ago - Stars: 33 - Forks: 7

open2c/quaich

snakemake pipeline for Hi-C post-processing

Language: Python - Size: 221 KB - Last synced at: 2 months ago - Pushed at: 12 months ago - Stars: 22 - Forks: 6

pneuvial/adjclust

Adjacency-constrained hierarchical clustering of a similarity matrix

Language: R - Size: 18.5 MB - Last synced at: 3 days ago - Pushed at: 9 months ago - Stars: 16 - Forks: 8

higlass/higlass-docker

Builds a docker container wrapping higlass-server and higlass-client in nginx

Language: Shell - Size: 5.66 MB - Last synced at: 2 months ago - Pushed at: about 3 years ago - Stars: 32 - Forks: 14

hanjunlee21/Lee-et-al-2023

RB represses cohesin-dependent loop formation and safeguards E2F-independent transcription

Language: Jupyter Notebook - Size: 70.4 MB - Last synced at: 3 days ago - Pushed at: 9 months ago - Stars: 1 - Forks: 0

4dn-dcic/docker-4dn-hic

Docker for 4DN Hi-C processing pipeline

Language: Common Workflow Language - Size: 527 MB - Last synced at: 7 months ago - Pushed at: 7 months ago - Stars: 58 - Forks: 18

robomics/call_tad_cliques

Nextflow workflow to call TAD cliques

Language: Python - Size: 194 KB - Last synced at: 9 months ago - Pushed at: 9 months ago - Stars: 1 - Forks: 0

Siegel-Lab/BioSmoother

On-the-fly processing and visualization of interactome data

Language: Python - Size: 36 MB - Last synced at: 11 months ago - Pushed at: 11 months ago - Stars: 4 - Forks: 0

Siegel-Lab/libBioSmoother

On-the-fly processing and visualization of interactome data.

Language: C++ - Size: 32.7 MB - Last synced at: 11 months ago - Pushed at: 11 months ago - Stars: 0 - Forks: 1

higlass/higlass-server

Server component for HiGlass that manages and serves tiled data

Language: Python - Size: 125 MB - Last synced at: 2 months ago - Pushed at: about 2 years ago - Stars: 19 - Forks: 21

mderakh3/IBD_variants-to-gene-mapping

Source code for uncovering IBD risk-driving regulatory mechanisms within different immune cell types

Language: R - Size: 181 KB - Last synced at: 11 months ago - Pushed at: 11 months ago - Stars: 0 - Forks: 0

roybarkan2020/AbsGenome

Genome assembly steps (Haliotis asinina)

Size: 2.6 MB - Last synced at: 11 months ago - Pushed at: 11 months ago - Stars: 2 - Forks: 0

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: Python - Size: 363 MB - Last synced at: 11 months ago - Pushed at: 11 months ago - Stars: 100 - Forks: 61

lanl/SLUR-M-py

SLUR(M)-py (pronounced slurpy): A SLURM Powered Pythonic Pipeline for Parallel Processing of 3D (Epi)genomic Profiles

Language: Python - Size: 203 KB - Last synced at: 3 months ago - Pushed at: 11 months ago - Stars: 1 - Forks: 0

Gabrielstav/mastercode

Code for my Master project

Language: Python - Size: 1.55 MB - Last synced at: 12 months ago - Pushed at: 12 months ago - Stars: 3 - Forks: 1

4DNucleome/tad_compare

Compare different sets of TADs inferred from Hi-C data (or other 3C technique) using different methods.

Language: Python - Size: 97.7 KB - Last synced at: about 1 year ago - Pushed at: about 4 years ago - Stars: 1 - Forks: 2

dyxstat/ImputeCC

ImputeCC enhances integrative Hi-C-based metagenomic binning through constrained random-walk-based imputation

Language: Python - Size: 4.9 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 1 - Forks: 1

koszullab/pareidolia

Multi-sample change detection in Hi-C patterns

Language: Python - Size: 1.19 MB - Last synced at: about 1 month ago - Pushed at: over 3 years ago - Stars: 9 - Forks: 3

ytanaka-bio/cisMultiDeep

Workflow to identify functional cis-regulatory regions for each annotated cell type

Language: Python - Size: 830 KB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0

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

aleskunder/topology_loop_caller

Chromatin loop caller using Topological Data Analysis based on Hi-C data

Language: Python - Size: 625 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 3 - Forks: 1

yufanzhouonline/HiSIF

HiSIF: Genome-wide chromatin interactions identify characteristic promoter-distal loops

Language: C++ - Size: 140 MB - Last synced at: 4 months ago - Pushed at: 9 months ago - Stars: 1 - Forks: 0

hms-dbmi/hic-data-analysis-bootcamp

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

Language: Jupyter Notebook - Size: 291 MB - Last synced at: about 1 year ago - Pushed at: about 7 years ago - Stars: 185 - Forks: 46

SmythLab/diffHicUsersGuide

Source code and comments for the diffHic user's guide.

Language: TeX - Size: 414 KB - Last synced at: about 1 year ago - Pushed at: over 7 years ago - Stars: 0 - Forks: 0

flekschas/hipiler-server 📦

[OUTDATED: Use HiGlass Server instead] The HiPiler Server

Language: Python - Size: 46.9 KB - Last synced at: over 1 year ago - Pushed at: almost 8 years ago - Stars: 1 - Forks: 0

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

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

Language: Jupyter Notebook - Size: 188 MB - Last synced at: about 1 year ago - Pushed at: almost 8 years ago - Stars: 48 - Forks: 9

foerstner-lab/HiCsuntdracones

HiC sunt dracones - or HiCDS in short - Your little helper for the HiC analysis

Language: Python - Size: 273 KB - Last synced at: over 1 year ago - Pushed at: almost 3 years ago - Stars: 0 - Forks: 1

OluwadareLab/TADMaster

TADMaster: A Comprehensive Web-based Tool For Analysis of Topologically Associated Domains

Language: Python - Size: 81.4 MB - Last synced at: about 1 year ago - Pushed at: over 2 years ago - Stars: 2 - Forks: 1

nlawlor/Multiomic_Browser

An R shiny application for visualization of EndoC-bH1 and human islet genomic data

Language: R - Size: 18 MB - Last synced at: over 1 year ago - Pushed at: over 6 years ago - Stars: 1 - Forks: 1

dozmorovlab/HiCcompare

Joint normalization of two Hi-C matrices, visualization and detection of differential chromatin interactions. See multiHiCcompare for the analysis of multiple Hi-C matrices

Language: R - Size: 82.8 MB - Last synced at: about 1 year ago - Pushed at: about 2 years ago - Stars: 15 - Forks: 3

deeptools/HiCBrowser

Simple web browser to visualize HiC tracks

Language: JavaScript - Size: 17.6 MB - Last synced at: about 1 year ago - Pushed at: over 5 years ago - Stars: 17 - Forks: 5

insilicoconsulting/snake-chic

Snakemake wrapper around the Arima Capture Hi-C (CHiC) workflow

Language: Python - Size: 8.79 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 2 - Forks: 0

4dn-dcic/pairsqc

QC report generator for Hi-C pairs file

Language: HTML - Size: 37.8 MB - Last synced at: over 1 year ago - Pushed at: almost 5 years ago - Stars: 10 - Forks: 2

vaquerizaslab/chess

Comparison of Hi-C Experiments using Structural Similarity.

Language: Python - Size: 241 MB - Last synced at: 11 months ago - Pushed at: almost 2 years ago - Stars: 26 - Forks: 6

rjdkmr/gcMapExplorer

Genome Contact Map Explorer - gcMapExplorer. Visit:

Language: Python - Size: 5.05 MB - Last synced at: 12 days ago - Pushed at: over 3 years ago - Stars: 21 - Forks: 9

ay-lab/dcHiC

dcHiC: Differential compartment analysis for Hi-C datasets

Language: R - Size: 155 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 44 - Forks: 9