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bcftools

This is the official development repository for BCFtools. To compile, the develop branch of htslib is needed: git clone --branch=develop git://github.com/samtools/htslib.git htslib

bowen_maizi

cnv_facets

Somatic copy variant caller (CNV) for next generation sequencing

corto

corto (Correlation Tool): an R package to generate correlation-based DPI networks

epilogos

fftw3

DO NOT CHECK OUT THESE FILES FROM GITHUB UNLESS YOU KNOW WHAT YOU ARE DOING. (See below.)

fithic

Fit-Hi-C is a tool for assigning statistical confidence estimates to chromosomal contact maps produced by genome-wide genome architecture assays such as Hi-C.

genmap

GenMap - Fast and Exact Computation of Genome Mappability

hicdat

Hi-C data analysis tool

hicdb

detect and visualize contact domain boundaries (CDBs) or differential CDBs from Hi-C (matlab version)

hicexplorer

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

hicplotter

“When everything is connected to everything else, for better or worse, everything matters.” Bruce Mau

imp

The Integrative Modeling Platform

mrtadfinder

a method to identify TADs in Hi-C data

nuc_dynamics

Particle dynamics and simulated annealing for chromosome structure calculation

nuc_processing

Chromatin contact paired-read single-cell Hi-C processing module for Nuc3D and NucTools

p3d

Plant 3D (P3D): A plant phenotyping toolkit for 3D point clouds

shortstack

ShortStack: Comprehensive annotation and quantification of small RNA genes

speedseq

A flexible framework for rapid genome analysis and interpretation

sra-tools

SRA Tools

tadtool

TADtool is an interactive tool for the identification of meaningful parameters in TAD-calling algorithms for Hi-C data.

tadtree