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NeoLoopFinder

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

CEMBA_wmb_snATAC

Whole mouse brain snATAC seq analysis

HiCLift

A fast and efficient tool for converting chromatin interaction data between genome assemblies

dip-c

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

scHiCluster

cooltools

The tools for your .cool's

STAR

RNA-seq aligner

sci-RNA-seq3_pipeline

Processing pipeline scripts for sci-RNA-seq3 (bash, R, python)

epiformer

cellranger

10x Genomics Single Cell Analysis

cooler

A cool place to store your Hi-C

cemba_data

Mapping pipeline for snmC-seq based technologies.

Higashi

single-cell Hi-C, scHi-C, Hi-C, 3D genome, nuclear organization, hypergraph

Fast-Higashi

single-cell Hi-C, scHi-C, Hi-C, 3D genome, nuclear organization, tensor decomposition

deeplearningbook-chinese

Deep Learning Book Chinese Translation

pairtools

Extract 3D contacts (.pairs) from sequencing alignments

tome_code

The scripts used for the analyses in TOME project

awesome-bioinformatics-benchmarks

A curated list of bioinformatics bench-marking papers and resources.

ailab

SnapATAC2

Single-cell epigenomics analysis tools

snATACutils

seurat

R toolkit for single cell genomics

bypass-paywalls-chrome

Bypass Paywalls web browser extension for Chrome and Firefox.

scChromHMM

🧬 🦀 A fast and efficient tool to perform a genome wide Single cell Chromatin State Analysis using multimodal histone modification data.

Paired-Tag

Analysis of Paired-Tag datasets

BMS_bioinformatics_bootcamp_2018

Class materials for the bioinformatics portion of BIOM 200, Fall 2018