In situ single cell spatial transcriptomics technologies are maturing from proof of concept demos into tools for exploring biological hypotheses. While many approaches for testing those hypotheses are adapted from single cell RNAseq, others are spatially focussed tests new to the transcriptomics field. This means many hours of bioinformatics analysis time invested in understanding these statistical tests so they can be correctly applied to a given research question. Often this entails a frustrating search across multiple packages, sifting through vignettes that describe a package in the context of older technologies or simplified examples.
Can we instead browse a smorgasbord of ‘hypothesis-first’ how-tos based on real spatial datasets? To this end, we are developing the ‘spatial snippets’ collection; a searchable, visual gallery where methods for testing common spatial and single cell RNA hypotheses are explained and demonstrated on real public data. Each example is standardised; featuring a description, diagram, concrete example on a real dataset, a code snippet, full explanation of output and further reading.
The goal is for these examples to provide a starting point for researchers new to the area, and give experienced bioinformaticians a useful code snippet to quickly adapt. These examples may also be translated into short intermediate training workshops. We hope to establish an open, citable community resource with contributions from bioinformaticians, trainers and tool developers. Available at: https://swbioinf.github.io/spatialsnippets/index.html