Below are some tutorials and workshop materials for getting started in single-cell spatial analyses. These all cover QC and preprocessing in some form.
An extensive vignette on single cell spatial omics analysis using the ‘SCDNEY’ collection of bioconductor packages. Covers the loading of image based data (of particular interest to protein imaging methods), through to QC and preprocessing and downstream analyses equally applicable to transcriptome based technologies.
Intro to spatial transcriptomics
Training materials for an introductory spatial transcriptomics workshop. This workshop demonstrates spatial pre-processing and QC steps in Seurat on the same Garrido-Trigo et al. 2023 IBD dataset used extensively within spatial sampler. It includes a section on how to practically tackle celltype annotation.
Voyager website : Analysis vignettes are listed by technology for for Xenium, cosmx, vizgen/merscope and others.
Not a tutorial per se, but a collection of useful vignettes for loading, QC, processing and testing data using the voyager package. Part of the bioconductor ecosystem, voyager uses the ‘SpatialFeatureExperiment’ object that builds on ‘SpatialExperiment’. Voyager functions focus on implementing spatial tests, and also provide some useful plotting functions.
OSTA (Orchestrating Spatial Transcriptomics Analysis with Bioconductor
A detailed resource on how to perform spatial analyses using the bioconductor ecosystem of packages. This is a useful resource for detailed explanations of analysis tasks.
OSCA - (Orchestrating Single Cell Analayis with bioconductor )
A detailed resource on single cell analyses using the bioconductor ecosystem of packages. Many of these tools and approaches can be directly applied to a spatial spatial analyses.
Seurat Imaging based spatial vignette
The seurat vignette for spatial analysis, covering how to load data from a number of technologies. ( NB: See ticket for further info on cosmx data loading.)
Spatial taster workshop materials
Training materials (Rmd files only) for an intermediate spatial transcriptomics workshop for comparative analyses using bioconductor packages. It again uses the the same Garrido-Trigo et al. 2023 IBD dataset used extensively within spatial sampler, and walks through differential expression by celltype, defining region niches and using those for differential expression by localisation, and celltype proximity tests.