SubcellularSpatialData (original) (raw)

This is the released version of SubcellularSpatialData; for the devel version, seeSubcellularSpatialData.

Annotated spatial transcriptomics datasets from 10x Xenium, NanoString CosMx and BGI STOmics.

Bioconductor version: Release (3.21)

This is a data package that hosts annotated sub-cellular localised datasets from the STOmics, Xenium and CosMx platforms. Specifically, it hosts datasets analysed in the publication Bhuva et. al, 2024 titled "Library size confounds biology in spatial transcriptomics data". Raw transcript detections are hosted and functions to convert them to SpatialExperiment objects have been implemented.

Author: Dharmesh D. Bhuva [aut, cre] ORCID: 0000-0002-6398-9157

Maintainer: Dharmesh D. Bhuva <dharmesh.bhuva at adelaide.edu.au>

Citation (from within R, enter citation("SubcellularSpatialData")):

Installation

To install this package, start R (version "4.5") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("SubcellularSpatialData")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("SubcellularSpatialData")

Details

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Package Archives

Follow Installation instructions to use this package in your R session.