Single Cell

scGPTJupyter Notebook

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

CellTypistPython

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

GLUEPython

A deep learning framework for integrating single-cell multi-omics data using graph-linked unified embeddings.

scMulanJupyter Notebook

A multitask generative pre-trained language model for zero-shot cell type annotation, batch integration, and conditional cell generation in single-cell transcriptomics.

BABELJupyter Notebook

A deep learning model that translates between single-cell multi-omic profiles, such as scATAC-seq and scRNA-seq, using a shared latent representation.

ChatSpatialPython

An MCP server that enables natural language conversation for analyzing spatial transcriptomics data through 60+ curated methods.

FlashDeconvPython

A fast spatial deconvolution tool for transcriptomics data that scales to million-spot datasets while preserving rare cell type signals.