lmweber/OSTA

This repository contains scNotebooks, a collection of interactive Jupyter and Google Colab notebooks designed to teach and practice single‑cell and spatial transcriptomics. The notebooks guide learners through the complete workflow from introductory steps and single‑cell pipelines to diverse analytical approaches, and FAIR and sharing data

A novel machine learning pipeline to analyse spatial transcriptomics data

STAgent is a multimodal LLM-based AI agent that enables deep research about spatial transcriptomics data

List of Spatial Transcriptomics related Tools organized per category

Code for the spatialLIBD R/Bioconductor package and shiny app

Graph-based foundation model for spatial transcriptomics data. Zero-shot spatial domain inference, batch-effect correction, and many other features.

This repository is an exploratory resource to accelerate opensource analysis of CosMx® Spatial Molecular Imager (SMI) data. Contained here are and writeups and vignettes addressing a variety of topics discussed when analyzing single-cell spatial data.

Spatial omics analysis toolbox