Chip Seq Python Packages

deeptools

Tools to process and analyze deep sequencing data.

macs3

MACS -- Model-based Analysis of ChIP-Seq

macs2

MACS -- Model-based Analysis of ChIP-Seq

rocco

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

rgt

Toolkit to perform regulatory genomics data analysis

pymasc

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

pygtftk

The Python GTF toolkit (pygtftk) package: easy handling of GTF files

bioepic

Chip-Seq broad peak/domain finder.

zen-norm

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

ngs-toolkit

A toolkit for NGS analysis with Python

moca

Tool for motif conservation analysis

manorm

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

pybedgraph

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

panchip

Pan-ChIP-seq Analysis of Peak Sets

mamotif

An integrative toolkit for detecting cell type-specific regulators

fseq2

Improving the feature density based peak caller with dynamic statistics

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