Scanpy

scGPTbowang-lab/scGPT

A transformer-based foundation model pretrained on millions of single-cell profiles for generative AI tasks in single-cell multi-omics.

Squidpyscverse/squidpy

A scalable Python toolkit for analyzing and visualizing spatial molecular data from tissue sections.

CellTypistTeichlab/celltypist

An automated cell type annotation tool for single-cell RNA-seq data using logistic regression classifiers.

scIB (Single-cell Integration Benchmarks)theislab/scib

A Python package for benchmarking and evaluating single-cell genomics data integration methods.

GEARSsnap-stanford/GEARS

A geometric deep learning model that predicts transcriptional outcomes of single and multi-gene perturbations from single-cell RNA-seq data.

scBERTTencentAILabHealthcare/scBERT

A BERT-based foundation model pretrained on large-scale scRNA-seq data for automated cell type annotation in single-cell analysis.