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SubcellularSpatialData

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 adelaide.edu.au>

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

Installation

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


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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")
SubcellularSpatialData HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews ExperimentData, ExperimentHub, Homo_sapiens_Data, LungCancerData, Mus_musculus_Data, SpatialData
Version 1.1.0
License GPL (>= 3)
Depends R (>= 4.4)
Imports dplyr, hexbin, Matrix, SpatialExperiment, stats
System Requirements
URL https://davislaboratory.github.io/SubcellularSpatialData
Bug Reports https://github.com/DavisLaboratory/SubcellularSpatialData/issues
See More
Suggests BiocStyle, ExperimentHub, ggplot2, knitr, prettydoc, rmarkdown, testthat (>= 3.0.0)
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Depends On Me
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Package Archives

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

Source Package SubcellularSpatialData_1.1.0.tar.gz
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/SubcellularSpatialData
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/SubcellularSpatialData
Package Short Url https://bioconductor.org/packages/SubcellularSpatialData/
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