SFEData

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

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16

Example SpatialFeatureExperiment datasets

Bioconductor version: Release (3.23)

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

Maintainer: Lambda Moses <dlu2 at caltech.edu>

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

Lambda Moses, Alik Huseynov, Kayla Jackson, Lior Pachter. SFEData: Example SpatialFeatureExperiment datasets. doi:10.18129/B9.bioc.SFEData, R package version 1.14.0, https://bioconductor.org/packages/SFEData.

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")

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	1.14.0
In Bioconductor since	BioC 3.16 (R-4.2) (4 years)
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
Build Report	Build Report, r-universe

Package Archives

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

Source Package	SFEData_1.14.0.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/SFEData
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/SFEData
Package Short Url	https://bioconductor.org/packages/SFEData/
Package Downloads Report	Download Stats