Scatac Seq Python Packages

crested

CREsted is a Python package for training sequence-based deep learning models on scATAC-seq data, for capturing enhancer code and for designing cell type-specific sequences.

muon

muon is a multimodal omics Python framework

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.

scatac-fragment-tools

Tools for working with scATAC-seq fragment files

scarf

Scarf: A scalable tool for single-cell omics data analysis

scperturb

scPerturb: A resource and a python/R tool for single-cell perturbation data

pychromvar

A python package for chromVAR

cell-tools

Single-Cell Data Analysis Tools

chame

Chromatin analysis module

epione

Analysis of epigenetic data in Python

sc-tools

Single-Cell Data Analysis Tools

scarf-toolkit

Toolkit for highly memory efficient analysis of single-cell RNA-Seq, scATAC-Seq and CITE-Seq data. Analyze atlas scale datasets with millions of cells on laptop.