scverse/spatialdata-tutorials

An open and interoperable data framework for spatial omics data

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

Interactive visualization of spatial omics data

Notebooks used in scvi-tools tutorials

"Orchestrating Spatial Transcriptomics Analysis with Bioconductor" (OSTA) online book

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.

Code for the spatialLIBD R/Bioconductor package and shiny app

TissUUmaps is a browser-based tool for fast visualization and exploration of millions of data points overlaying a tissue sample. TissUUmaps can be used as a web service or locally in your computer, and allows users to share regions of interest and local statistics.