Single Cell Omics Python Packages

cellestial

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

pixelgen-pixelator

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

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.

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.

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.

randomly

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

pamona

manifold alignment method for single-cell multi-omics integration using Pamona

scomix

Single-Cell Data Science