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

doubletdetection

Doublet detection in single-cell RNA-seq data.

autozyme

Autonomous multi-agent framework to optimize scientific software

palantir

Single cell trajectory detection

kb-python

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

cirrocumulus

Bring your single-cell data to life

scarches

Reference mapping for single-cell genomics

tangram-sc

Spatial alignment of single cell transcriptomic data.

cellmapper

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

cellxgene

An interactive explorer for single-cell transcriptomics data

scgen

Single cell perturbation prediction

scvi

Deep probabilistic analysis of single-cell and spatial omics data

dynamo-release

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

scdef

Deep exponential families for single-cell data.

desc

Deep Embedding for Single-cell Clustering

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.

larry-dataset

LARRY Dataset: lineage and RNA recovery

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.

scembed

Run embedding comparisons for single-cell data

cell-annotator

Automatically annotate cell types, consistently across samples.

normalisr

Causal inference, differential expression, and co-expression for scRNA-seq

dotools-py

Convenient and user-friendly package to streamline common workflows in single-cell RNA sequencing data analysis