Single Cell Omics Python Packages

scarf

Memory-efficient single-cell analysis in Python. Stream RNA, ATAC, CITE-seq and multi-omics from local or remote Zarr stores, from laptop to atlas scale, with reusable fingerprinted results.

univi

UniVI is a scalable multi-modal VAE toolkit for aligning heterogeneous single-cell datasets into a shared latent space—supporting unimodal, dual-modal, and tri-modal (and beyond) integration. It can additionally be used for cross-modal imputation, data generation of biologically-relevant synthetic samples, data denoising, and structured evaluation.

cellestial

An Interactive and Highly Customizable Single-Cell and Spatial Biology Plotting Library

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.

pixelgen-pixelator

A command-line tool and library to process and analyze sequencing data from Molecular Pixelation (MPX) and Proximity Network (PNA) assays.

scyan

Biology-driven deep generative model for cell-type annotation in cytometry. Scyan is an interpretable model that also corrects batch-effect and can be used for debarcoding or population discovery.

nichenetpy

nichenetpy: the python implementation of the NicheNet method. The goal of NicheNet is to study intercellular communication from a computational perspective. NicheNet uses human or mouse gene expression data of interacting cells as input and combines this with a prior model that integrates existing knowledge on ligand-to-target signaling paths. This allows to predict ligand-receptor interactions that might drive gene expression changes in cells of interest.

cytearc

Fast, out-of-core single-cell analysis in Python for RNA, ATAC, protein, and multi-omic data, scaling to 100M+ cells. Mount remote datasets, work within a memory budget, and trace every result through built-in provenance.

cell-decipher

DECIPHER for learning high-fidelity disentangled embeddings from spatial omics data

scoit

SCOIT is an implementation of a probabilistic tensor decomposition framework for single-cell multi-omics data integration.

pamona

The software of Pamona, a partial manifold alignment algorithm.

randomly

A Library for Denoising Single-Cell Data with Random Matrix Theory

scomix

Single-Cell Data Science