Single Cell Rna Seq Python Packages

squidpy

Spatial Single Cell Analysis in Python

scvi-tools

Deep probabilistic analysis of single-cell and spatial omics data

liana

LIANA+: an all-in-one framework for cell-cell communication

brisc

Fast single-cell toolkit

divik

Divisive Intelligent K-Means algorithm (DiviK) for joint feature selection and clustering of heavily multidimensional data.

cellrank

CellRank: dynamics from multi-view single-cell data

kb-python

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

ambidose

AmbiDose is a conservative, cell-aware Python toolkit for ambient RNA correction in droplet scRNA-seq. It estimates sample-specific ambient profiles and per-cell doses, protects native cell-type signals, preserves sparsity, and never inflates counts.

crest-sc

Chunked Rust Engine for Single-cell Transcriptomics

polariseq

Atlas-scale single-cell RNA-seq analysis in Python with a Rust core. Plans memory before reading; runs in memory or out of core.

piaso-tools

PIASO: Precise Integrative Analysis of Single-cell Omics

laris

LARIS maps ligand-receptor signalling in spatial transcriptomics within and across tissue states

hide-deconv

Hierarchical cell-type deconvolution and analysis of bulk RNA-seq data using single-cell references | Python package and CLI

cytome

Single-file format for single-cell multi-omics and spatial transcriptomics — matrices, metadata, embeddings, fragments and provenance in one SQLite-backed .cytome file, with SQL metadata queries and genomic range indexes.

scxpand

scXpand: detection of T-cell clonal expansion from single-cell RNA sequencing

sccoda

A Bayesian model for compositional single-cell data analysis

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.

scvi

Deep probabilistic analysis of single-cell and spatial omics data

scdef

Deep exponential families for single-cell data.

scxpand-cuda

scXpand: detection of T-cell clonal expansion from single-cell RNA sequencing

cosg

Accurate and fast cell marker gene identification with COSG

scdataloader

a dataloader to work with large single cell datasets from lamindb

toolchest-client

Toolchest Python client

scatrans

A Python package for mechanism-aware single-cell differential analysis. It partitions DE genes into transcription-driven versus stabilization-driven classes using nascent (unspliced) RNA residuals. Also supports conventional DE, functional enrichment (ORA, GSEA, GO, KEGG), and visualization.