Scrna Seq Python Packages

scvi-tools

Deep probabilistic analysis of single-cell and spatial omics data

palantir

Single cell trajectory detection

celltypist

A tool for semi-automatic cell type classification

brisc

Fast single-cell toolkit

muon

muon is a multimodal omics Python framework

stpipeline

ST Pipeline contains the tools and scripts needed to process and analyze the raw files generated with the Spatial Transcriptomics method in FASTQ format.

kb-python

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

pertpy

Single-cell perturbation analysis

cirrocumulus

Bring your single-cell data to life

doubletdetection

Doublet detection in single-cell RNA-seq data.

metalcyte

Fast single-cell RNA-seq analysis on Apple silicon Macs, with a Rust engine, Metal GPU kernels and support for datasets larger than memory

dynamo-release

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

cellxgene

An interactive explorer for single-cell transcriptomics data

autozyme

Autonomous multi-agent framework to optimize scientific software

tangram-sc

Spatial alignment of single cell transcriptomic data.

scarches

Reference mapping for single-cell genomics

piaso-mcp

Agent-neutral knowledge hub that makes the PIASO single-cell omics ecosystem (PIASO, COSG/COSGR, LARIS, Emergene, PIASOmarkerDB) first-class for any coding agent. One canonical source generates Claude skills, Cursor rules, AGENTS.md, llms.txt, and an MCP server.

cellmapper

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

scvi

Deep probabilistic analysis of single-cell and spatial omics data

scdef

Deep exponential families for single-cell data.

rustscenic

Fast, memory-efficient tools for studying gene regulation in single-cell data, built with Rust and Python.

vireosnp

Demultiplexing pooled scRNA-seq data with or without genotype reference

clonetrast

CloneTrast reveals pan-cancer clonal niches of T-cells from single-cell RNA sequencing using contrastive learning

desc

Deep Embedding for Single-cell Clustering