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This is the development version of SubcellularSpatialData; for the stable release version, see SubcellularSpatialData.

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

Bioconductor version: Development (3.20)

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]

Maintainer: Dharmesh D. Bhuva <dharmesh.bhuva at>

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


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


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


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

SubcellularSpatialData HTML R Script
Reference Manual PDF


biocViews ExperimentData, ExperimentHub, Homo_sapiens_Data, LungCancerData, Mus_musculus_Data, SpatialData
Version 1.1.3
License GPL (>= 3)
Depends R (>= 4.4)
Imports dplyr, hexbin, Matrix, SpatialExperiment, stats
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Suggests BiocStyle, ExperimentHub, ggplot2, knitr, prettydoc, rmarkdown, testthat (>= 3.0.0)
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Follow Installation instructions to use this package in your R session.

Source Package SubcellularSpatialData_1.1.3.tar.gz
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