3d-genome 开源项目推荐（68 个）

mdozmorov /HiC_tools

A collection of tools for Hi-C data analysis

aidenlab /juicer

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

open2c /cooler

一个很酷的地方存放你的Hi-C。

open2c /pairtools

Extract 3D contacts (.pairs) from sequencing alignments

YaqiangCao /cLoops

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

ma-compbio /Higashi

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

XiaoTaoWang /HiCLift

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

YaqiangCao /cLoops2

增强且优雅的灵活峰值/环路/域调用和分析工具，用于1D/3D基因组数据。

ma-compbio /MATCHA

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

jasonwong-lab /gghic

gghic makes visualization of Hi-C/-like data easily in R

ma-compbio /SNIPER

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

kundajelab /genomedisco

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

ma-compbio /Fast-Higashi

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

ma-compbio /scGHOST

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

ma-compbio /Phylo-HMRF

该项目在 GitHub 上没有填写描述

Tian-Dechao /diffDomain

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

ma-compbio /GAGE-seq

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

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

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

anyuzx /HIPPS-DIMES

4D Genome Reconstruction and Dynamics Prediction: Maximum Entropy Based HI-C/Distance Map - Polymer Physics - Structures Method

data-fun /3d-genome-builder

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