Atac Seq Python Packages

macs3

MACS -- Model-based Analysis of ChIP-Seq

rocco

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

macs2

MACS -- Model-based Analysis of ChIP-Seq

circe-py

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

rustscenic

Rust + PyO3 reimplementation of the SCENIC+ single-cell regulatory-network pipeline. ATAC preproc, peak calling, GRN, AUCell, topics, cistarget, eRegulon — one pip install, no Java, no MACS2, no dask.

atacfragqc

QC for ATAC-seq fragments

rgt

Toolkit to perform regulatory genomics data analysis

tobias

Transcription factor Occupancy prediction By Investigation of ATAC-seq Signal

ngs-toolkit

A toolkit for NGS analysis with Python

bintogene

A bin to gene conversion package.

zen-norm

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

recon

ReCoN: [Reconstruction of multicellular systems from single-cell data to predict perturbation responses and cell programs coordination]

pybedgraph

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

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

maxatac

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

nucleoatac

python package for calling nucleosomes with ATAC-Seq

chame

Chromatin analysis module

cisvar

cisVar scripts.