hi-c 开源项目推荐（217 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

maxplanck-ie /snakepipes

基于 snakemake 和 python 的可定制工作流程，用于分析 NGS 数据

higlass /higlass

Fast, flexible and extensible genome browser.

zengxiaofei /HapHiC

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

open2c /cooler

一个很酷的地方存放你的Hi-C。

hms-dbmi /hic-data-analysis-bootcamp

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

mdozmorov /HiC_data

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

open2c /pairtools

Extract 3D contacts (.pairs) from sequencing alignments

lh3 /hickit

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

wangyibin /CPhasing

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

YaqiangCao /cLoops

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

nf-core /hic

Analysis of Chromosome Conformation Capture data (Hi-C)

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 f…

open2c /distiller-nf

A modular Hi-C mapping pipeline

4dn-dcic /pairix

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

robinweide /GENOVA

GENome Organisation Visual Analytics

tanjimin /C.Origami

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

ay-lab /mustache

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

open2c /coolpuppy

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