hic 开源项目推荐（73 个）

deeptools /HiCExplorer

HiCExplorer is a powerful and easy to use set of tools to process, normalize and visualize Hi-C data.

marbl /SALSA

SALSA: A tool to scaffold long read assemblies with Hi-C data

wangyibin /CPhasing

C-Phasing/CPhasing: Phasing and scaffolding polyploid genomes based on 3C-based data (Pore-C, CiFi, Hi-C, Omni-C).

paulsengroup /hictk

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

ctlab /HiCT_JVM

Interactive visualizer and manual scaffolder of Hi-C contact maps. All-in-one Java-based implementation.

junjunlab /BioSeqUtils

Extract Sequence from Genome According to Annotation File

omegahh /DeepHiC

基于GAN的Hi-C数据增强方法

jasonwong-lab /gghic

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

sanger-tol /genomenote

Nextflow DSL2 pipeline to generate a Genome Note, including assembly statistics, quality metrics, and Hi-C contact maps. This workflow is part of the Tree of Life production suite.

kundajelab /genomedisco

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

ren-lab /hic-pipeline

该项目在 GitHub 上没有填写描述

HenrikBengtsson /TopDom

R package: TopDom - An efficient and Deterministic Method for identifying Topological Domains in Genomes

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

paulsengroup /modle

High-performance stochastic modeling of DNA loop extrusion interactions

paulsengroup /hictkpy

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

sanger-tol /curationpretext

A Nextflow DSL2 pipeline for pretext generation in curation

data-fun /3d-genome-builder

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

nf-core /hicar

Pipeline for HiCAR data, a robust and sensitive multi-omic co-assay for simultaneous measurement of transcriptome, chromatin accessibility and cis-regulatory chromatin contacts.

zqbake /hictools

Tools for processing HIC data.

wangyibin /C-Studio

C-Studio is a desktop app for visualizing and editing chromosome-scale genome assemblies with AGP layouts, 3D contact maps, synteny, and assembly-graph evidence.