Atac Seq Python Packages

consenrich

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

macs3

MACS -- Model-based Analysis of ChIP-Seq

macs2

MACS -- Model-based Analysis of ChIP-Seq

rocco

Multisample Consensus Peak Calling via Convex Optimization

circe-py

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

atacfragqc

QC for ATAC-seq fragments

rustscenic

Rust and PyO3 implementation of SCENIC-style regulatory-network analysis. Includes GRN, AUCell, topics, cistarget, peak calling, cell QC, enhancer-gene links, and eRegulon assembly. Installs without dask, Java, or CUDA.

tobias

Transcription factor Occupancy prediction By Investigation of ATAC-seq Signal

zen-norm

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

rgt

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

ngs-toolkit

A toolkit for NGS analysis with Python

bintogene

A bin to gene conversion package.

pybedgraph

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

asap-o-matic

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

recon

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

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 accessibility module

cisvar

Calculate both pre and post frequencies for ChIP or ATAC style data