PyRank

Hi C Python Packages

Python packages with the GitHub topic hi-c. Sorted by monthly downloads, with stars and forks.
open2c
cooler

A cool place to store your Hi-C

14K 245 62
open2c
pairtools

Extract 3D contacts (.pairs) from sequencing alignments

5K 138 39
koszullab
hicstuff

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

2K 42 9
Siegel-Lab
libbiosmoother

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

2K 0 1
higlass
clodius

Clodius is a tool for breaking up large data sets into smaller tiles that can subsequently be displayed using an appropriate viewer.

2K 40 22
rjdkmr
gcmapexplorer

Genome Contact Map Explorer - gcMapExplorer. Visit:

1K 23 9
koszullab
chromosight

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

1K 71 11
4dn-dcic
pypairix

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

1K 94 15
ay-lab
mustache-hic

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

1K 84 13
4dn-dcic
hic2cool

Lightweight converter between hic and cool contact matrices.

911 74 11
XiaoTaoWang
tadlib

A Library to Explore Chromatin Interaction Patterns for Topologically Associating Domains

721 45 13
koszullab
metator

Metagenomic binning based on Hi-C data

654 30 10
XiaoTaoWang
runhic

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

492 66 24
open2c
coolpuppy

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

486 82 12
seqyuan
trackc

trackc aims to produce beautiful genome tracks that are highly customizable

401 19 0
XiaoTaoWang
neoloop

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

330 78 18
adamyhe
ep-touche

Touché: scalable enhancer–promoter contact analysis for Micro-C and Hi-C data

311 1 0
vaquerizaslab
chess-hic

Comparison of Hi-C Experiments using Structural Similarity.

307 27 6
cmdoret
pareidolia

Multi-sample change detection in Hi-C patterns

301 9 3
XiaoTaoWang
hicpeaks

A Python implementation for BH-FDR and HiCCUPS

281 55 11
Siegel-Lab
biosmoother

On-the-fly processing and visualization of interactome data

265 6 0
Tian-Dechao
diffdomain-py3

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

241 18 5
cmdoret
hicreppy

Python reimplementation of hicrep with compatibility for sparse matrices

210 21 3
koszullab
instagraal

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

206 44 10