37 Open Source Chip Seq Software Projects

ChIP-seq analysis notes from Ming Tang

MACS -- Model-based Analysis of ChIP-Seq

Tools to process and analyze deep sequencing data.

Customizable workflows based on snakemake and python for the analysis of NGS data

A collection of Galaxy-related training material

AQUAS TF and histone ChIP-seq pipeline

a snakemake pipeline to process ChIP-seq files from GEO or in-house

ChIP-seq peak-calling, QC and differential analysis pipeline.

A graphical user interface for distributed data processing of high throughput genomics

Regulatory Genomics Toolbox: Python library and set of tools for the integrative analysis of high throughput regulatory genomics data.

Haystack: Epigenetic Variability and Transcription Factor Motifs Analysis Pipeline

Automated and customizable preprocessing of Next-Generation Sequencing data, including full (sc)ATAC-seq, ChIP-seq, and (sc)RNA-seq workflows. Works equally easy with public as local data.

(DEPRECATED) epic: diffuse domain ChIP-Seq caller based on SICER

Go / Golang Bioinformatics Library

Tools for querying and analysis of genomic data

deepStats: a stastitical toolbox for deeptools and genomic signals

Summer school course materials collection

ChIP-seq/RNA-seq analysis software suite for gene expression heatmaps

A python package and a set of shell commands to handle GTF files

CWL tools and workflows for GGR

A robust model for quantitative comparison of ChIP-Seq data sets.

A Python package for fast operations on 1-dimensional genomic signal tracks

API for HOMER in R for Genomic Analysis using Tidy Conventions

Reproducible reanalysis of a combined ChIP-Seq & RNA-Seq data set

AnaLysis routines for ePigenomicS data - 🏫 Bioconductor project

7C: Computational Chromosome Conformation Capture by Correlation of ChIP-seq at CTCF motifs

Pipelines for NGS data preprocessing by the Bock lab and friends

A toolkit for NGS analysis with Python

An automated ChIP-seq pipeline using Nextfow

Bioinformatics library in Kotlin

Publication quality NGS track plotting

An open-source and scalable solution to NGS analysis powered by the NIH's Biowulf cluster.

MAnorm2 for Normalizing and Comparing ChIP-seq Samples

AnceTran2.0: R package for transcriptome evolution analysis based on RNA-seq expression data or ChIP-seq TF-binding data

TFregulomeR reveals transcription factors’ context-specific features and functions

Using combined evidence from replicates to evaluate ChIP-seq peaks

Multi-omics analysis protocols by Lyu.