Chip Seq Python Packages

macs3

MACS -- Model-based Analysis of ChIP-Seq

consenrich

Genome-wide extraction of real-valued signals hidden in noisy multisample HTS data

deeptools

Tools to process and analyze deep sequencing data.

macs2

MACS -- Model-based Analysis of ChIP-Seq

rocco

Robust Open Chromatin Detection via Convex Optimization: Multisample Consensus Peak Calling

pymasc

Python implementation to calc mappability-sensitive cross-correlation for fragment length estimation and quality control for ChIP-Seq.

pygtftk

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

rgt

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

tfbs-footprinting3

Pipeline: Identification of cis-regulatory elements by matrix scoring and analysis of supporting empirical biological data.

bioepic

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

ngs-toolkit

A toolkit for NGS analysis with Python

panchip

Pan-ChIP-seq Analysis of Peak Sets

zen-norm

ZEN-norm is a Python package for normalising bigWigs of genomic signal, reversing prior normalisation and benchmarking normalisation method performance.

pybedgraph

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

manorm

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

moca

:m: Tool for motif conservation analysis

fseq2

Improving the feature density based peak caller with dynamic statistics

mamotif

An integrative toolkit for detecting cell type-specific regulators

seriesoftubes

Historical archive: Python 2.7-era UCSF ChIP-seq pipeline for Solexa data. Not maintained; kept for provenance.

manorm2-utils

To pre-process a set of ChIP-seq samples and coordinate with MAnorm2 for differential analysis

maxatac

Transcription Factor Binding Prediction from ATAC-seq and scATAC-seq with Deep Neural Networks