SFEData

This is the released version of SFEData; for the devel version, see SFEData.

Example SpatialFeatureExperiment datasets

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DOI: 10.18129/B9.bioc.SFEData

Bioconductor version: Release (3.22)

Example spatial transcriptomics datasets with Simple Feature annotations as SpatialFeatureExperiment objects. Technologies include Visium, slide-seq, Nanostring CoxMX, Vizgen MERFISH, and 10X Xenium. Tissues include mouse skeletal muscle, human melanoma metastasis, human lung, breast cancer, and mouse liver.

Author: Lambda Moses [aut, cre] ORCID iD ORCID: 0000-0002-7092-9427 , Alik Huseynov [aut] ORCID iD ORCID: 0000-0002-1438-4389 , Kayla Jackson [aut] ORCID iD ORCID: 0000-0001-6483-0108 , Lior Pachter [aut, ths] ORCID iD ORCID: 0000-0002-9164-6231

Maintainer: Lambda Moses <dlu2 at caltech.edu>

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

Installation

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


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

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("SFEData")

Example SpatialFeatureExperiment datasets HTML R Script

Reference Manual PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews ExperimentData, ExperimentHub, ExpressionData, Homo_sapiens_Data, Mus_musculus_Data, SingleCellData, SpatialData, Tissue

Version 1.12.0

License Artistic-2.0

Depends R (>= 4.1.0)

Imports BiocFileCache, AnnotationHub, ExperimentHub, utils

System Requirements

URL https://github.com/pachterlab/SFEData

Bug Reports https://github.com/pachterlab/SFEData/issues

Suggests BiocStyle, knitr, rmarkdown, SeuratObject, SpatialFeatureExperiment, testthat (>= 3.0.0)

Linking To

Enhances

Depends On Me

Imports Me OSTA

Suggests Me alabaster.sfe, concordexR, jazzPanda, SpatialFeatureExperiment, Voyager, xenLite

Links To Me

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Package Archives

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

Source Package SFEData_1.12.0.tar.gz

Windows Binary (x86_64)

macOS Binary (x86_64)

macOS Binary (arm64)

Source Repository git clone https://git.bioconductor.org/packages/SFEData

Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/SFEData

Package Short Url https://bioconductor.org/packages/SFEData/

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