SpaceBlocks¶
A Snakemake workflow for single-cell-resolution spatial transcriptomics.
This site documents SpaceBlocks, a technology-agnostic Snakemake workflow to semi-automatically analyse single-cell-resolution spatial transcriptomics (ST).
New here? Start taking a look at the configuration, follow with get started for a complete run and check the examples with public data.
Quickstart glossary¶
- HeadBlocks — technology-specific sets of rules that prepare the raw data files into a contract h5ad.
- CoreBlocks — technology-agnostic sets of rules that streamline ST processing steps.
- Contract — the standardized AnnData h5ad files, validated before running the CoreBlocks.
Full documentation:¶
- Configuration — explanation of all config keys and sample sheets.
- Get started: recommendations for a full run — how to streamline a full run.
- Demos — public data end-to-end example runs.
- QuPath annotation — tutorial to easily draw and export the region annotations.
- Workflow design, architectural decisions and output structure — a brief explanation on the HeadBlock/CoreBlock split, the contract, and output tree.
- Rule reference — every rule explained briefly, grouped by HeadBlock/CoreBlock phase.
- Outputs — what each step produces and why it is useful.
- Environments — the Conda environments and how to lock them.
- Source code: github.com/cbib/SpaceBlocks
- Snakemake Workflow Catalog: entry for SpaceBlocks