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

scatac-fragment-tools

Tools for working with scATAC-seq fragment files

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.

scarf

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.

pychromvar

A python package for chromVAR

scperturb

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

cell-tools

Single-Cell Data Analysis Tools

epione

Analysis of epigenetic data in Python

chame

Chromatin accessibility module

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.