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

🎯 ChIP peak Annotation, Comparison and Visualization

ChIP-seq peak-calling, QC and differential 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.

Publication quality NGS track plotting

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

AQUAS TF and histone ChIP-seq pipeline

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

Differential abundance analysis for feature/ observation matrices from platforms such as RNA-seq

Multi-omics analysis protocols by Lyu.

Haystack: Epigenetic Variability and Transcription Factor Motifs Analysis Pipeline

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

Go / Golang Bioinformatics Library

deepStats: a stastitical toolbox for deeptools and genomic signals

A Snakemake workflow and MrBiomics module for performing genomic region set and gene set enrichment analyses using LOLA, GREAT, GSEApy, pycisTarget and RcisTarget.

Extract Sequence from Genome According to Annotation File