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 (3.24)
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("SubcellularSpatialData")):Dharmesh D. Bhuva. SubcellularSpatialData: Annotated spatial transcriptomics datasets from 10x Xenium, NanoString CosMx and BGI STOmics. doi:10.18129/B9.bioc.SubcellularSpatialData, R package version 1.9.0, https://bioconductor.org/packages/SubcellularSpatialData.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
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 | ||
| NEWS | Text |
Details
| biocViews | ExperimentData, ExperimentHub, Homo_sapiens_Data, LungCancerData, Mus_musculus_Data, SpatialData |
| Version | 1.9.0 |
| In Bioconductor since | BioC 3.19 (R-4.4) (2.5 years) |
| 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) |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | SubcellularSpatialData_1.9.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | |
| macOS Binary (sonoma-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/ |
| Package Downloads Report | Download Stats |