Search Packages

macs2

MACS -- Model-based Analysis of ChIP-Seq

deeptools

Tools to process and analyze deep sequencing data.

macs3

MACS -- Model-based Analysis of ChIP-Seq

rocco

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

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.

pymasc

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

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

moca

:m: Tool for motif conservation analysis

zen-norm

Zone Equalisation Normalisation: A Python package for bigWig scaling

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.

fseq2

Improving the feature density based peak caller with dynamic statistics

mamotif

An integrative toolkit for detecting cell type-specific regulators

manorm2-utils

To pre-process a set of ChIP-seq samples

maxatac

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