Single Cell Analysis Python Packages

harmonypy

🎼 Integrate multiple high-dimensional datasets with fuzzy k-means and locally linear adjustments.

brisc

Fast single-cell toolkit

scimap

Spatial Single-Cell Analysis Toolkit

pycomplexheatmap

PyComplexHeatmap: A Python package to plot complex heatmap (clustermap)

spacr

spaCR Spatial phenotype analysis of CRISPR–Cas9 screens (spaCR)

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.

celescope

Single Cell Analysis Pipelines

piaso-tools

PIASO: Precise Integrative Analysis of Single-cell Omics

laris

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

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.

cytotable

Harmonize high-content image analysis tool outputs for processing with Pycytominer and other Cytomining tools.

qpsphere

Python library for spheres in quantitative phase imaging

cosg

Accurate and fast cell marker gene identification with COSG

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.

spatialprofilingtoolbox

Spatial Multiomics Profiler for Spatial Characterization of Tissue Microenvironment (https://smprofiler.io) [NeurIPS'26]

featuremap

FeatureMAP (Feature-preserving Manifold Approximation and Projection) is an interpratable dimensionality reduction tool.

mnnpy

An implementation of MNN (Mutual Nearest Neighbors) correct in python.

pypairs

PyPairs - A python scRNA-Seq classifier

sctape

Deep learning-based tissue compositions and cell-type-specific gene expression analysis with tissue-adaptive autoencoder (TAPE)

scslat

Spatial-Linked Alignment Tool

scportrait

scPortrait is a scalable toolkit to generate single-cell representations from raw microscopy images

emergene

Individual cell-based differential transcriptomic analysis across conditions

transmorph

Computational framework for dataset integration

ccsf

Leveraging cell-cell similarity for high-performance spatial and temporal cellular mappings from gene expression data (Cell Patterns, 2023)