Atac Seq Python Packages

macs3

MACS -- Model-based Analysis of ChIP-Seq

rustscenic

Rust and PyO3 implementation of SCENIC-style single-cell regulatory-network analysis. GRN, AUCell, topics, cisTarget, peak calling, cell QC, enhancer-gene links, and eRegulon assembly in one pip install.

macs2

MACS -- Model-based Analysis of ChIP-Seq

rocco

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

circe-py

Circe: Package for building co-accessibility networks from ATAC-seq data.

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

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.

ngs-toolkit

A toolkit for NGS analysis with Python

recon

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

pybedgraph

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

asap-o-matic

Rearrange ASAP-seq antibody reads into something Alevin can recognize and count.

fseq2

Improving the feature density based peak caller with dynamic statistics

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.