Scrna Seq Python Packages

scvi-tools

Deep probabilistic analysis of single-cell and spatial omics data

muon

muon is a multimodal omics Python framework

celltypist

A tool for semi-automatic cell type classification

palantir

Single cell trajectory detection

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.

cirrocumulus

Bring your single-cell data to life

doubletdetection

Doublet detection in single-cell RNA-seq data.

dynamo-release

Inclusive model of expression dynamics with conventional or metabolic labeling based scRNA-seq / multiomics, vector field reconstruction and differential geometry analyses

kb-python

A wrapper for the kallisto | bustools workflow for single-cell RNA-seq pre-processing

scarches

Reference mapping for single-cell genomics

cellxgene

Web application for exploration of large scale scRNA-seq datasets

scvi

Deep probabilistic analysis of single-cell and spatial omics data

tangram-sc

Spatial alignment of single cell transcriptomic data.

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.

desc

Deep Embedding for Single-cell Clustering

cellmapper

k-NN-based mapping of cells across representations to transfer labels, embeddings, and expression values.

scdef

Deep exponential families for single-cell data.

larry-dataset

Documentation associated with preparing and formatting datasets LARRY datasets for ML applications with pytorch / pytorch lightning

symphonypy

Port of symphony algorithm of single-cell reference atlas mapping to Python

cellxgene-gateway

Cellxgene Gateway

irescue

Uncertainty-aware quantification of Transposable Elements expression in scRNA-seq

scgen

Single cell perturbation prediction

scembed

Run embedding comparisons for single-cell data

came

cell-type assignment and gene module extraction of scRNA-seq