Atac Seq Python Packages

fp-tools-bio

Command-first ATAC-seq footprinting, motif analysis, and reproducible interactive reports

macs3

MACS -- Model-based Analysis of ChIP-Seq

consenrich

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

macs2

MACS -- Model-based Analysis of ChIP-Seq

rocco

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

atacfragqc

QC for ATAC-seq fragments

circe-py

Co-accessibility network from single-cell ATAC-seq data. Python code with AnnData, based on Cicero algorithm.

rustscenic

Fast, memory-efficient tools for studying gene regulation in single-cell data, built with Rust and Python.

tobias

Transcription factor Occupancy prediction By Investigation of ATAC-seq Signal

rgt

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

bintogene

A tool for replacing promoter accessibility with a gene activity score.

ngs-toolkit

A toolkit for NGS analysis with Python

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

recon

Exploring multicellular coordination from single-cell gene expression / multi-omics using mutlilayer network representations

fseq2

Improving the feature density based peak caller with dynamic statistics

asap-o-matic

Application reformat the antibody reads from ASAP-seq to match those from normal CITE-seq assays

nucleoatac

nucleosome calling using ATAC-seq

maxatac

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

chame

Chromatin analysis module

cisvar

cisVar scripts.