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3dchromatin_replicateqc

Software to compute reproducibility and quality scores for Hi-C data

blender-chemicals

Draws chemicals in Blender using common input formats (smiles, molfiles, cif files, etc.)

bwa

Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)

cell_down

download sequencing result from solargenomics and do md5sum check

chipseq

ChIP-seq peak-calling, QC and differential analysis pipeline (Snakemake port of the nextflow pipeline at https://nf-co.re/chipseq).

chromap

Fast alignment and preprocessing of chromatin profiles

clean_pairs

clean duplicate contacts or promiscuous legs in pairs file

coco_way

dip-c workflow without rna

codecasus

Notebooks on dealing with some annoying and tedious coding obstacles.

cooler

A cool place to store your Hi-C

cooltools

The tools for your .cool's

dip-c

Tools to analyze Dip-C (or other 3C/Hi-C) data

docker_files

drop-seq

Java tools for analyzing Drop-seq data

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.

fithic_workflow

use fit-Hi-C to call significant interactions

frp

A fast reverse proxy to help you expose a local server behind a NAT or firewall to the internet.

h-magma

hap.py

Haplotype VCF comparison tools

hapcut2

software tools for haplotype assembly from sequence data

hic_basic

hickit

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

hicpeaks

A Python implementation for BH-FDR and HiCCUPS

hicrep

R package to evaluate reproducibility of Hi-C data

hicstuff

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

higashi

higlass-python

Python bindings to and Jupyter Notebook+Lab integration for the HiGlass viewer

hint

HiC for copy Number variation and Translocation detection

hires_utils

scripts for hires pipline

mustache

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