OSTA.data

OSTA.data provides programmatic access to publicly available spatial transcriptomics and scRNA-seq datasets stored in an Open Storage Framework (OSF) repository for use in the Orchestrating Spatial Transcriptomics Analysis (OSTA) with Bioconductor online book.

Key Features:

• Multi-platform dataset coverage: Supports sequencing- and imaging-based platforms including Visium, Visium HD, Xenium (10x Genomics), CosMx (NanoString), and scRNA-seq (Chromium).
• OSF repository integration: Queries and retrieves data from a dedicated OSF node using functions from the osfr package.
• Local caching: Caches retrieved Zip archives using BiocFileCache for efficient data reuse.

Scientific Applications:

• Spot deconvolution: Provides scRNA-seq reference data for deconvolving spatial transcriptomics spots.
• Label transfer: Enables supervised clustering through cell type label transfer from scRNA-seq to spatial data.
• Spatial transcriptomics analysis education: Supplies example datasets for the OSTA with Bioconductor online book workflows.

Methodology:

Data are queried and downloaded from an OSF repository using the osfr package, and Zip archives are cached locally using BiocFileCache.