Package: SFEData 1.15.0

Lambda Moses

SFEData: Example SpatialFeatureExperiment datasets

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.

Authors:Lambda Moses [aut, cre], Alik Huseynov [aut], Kayla Jackson [aut], Lior Pachter [aut, ths]

SFEData_1.15.0.tar.gz
SFEData_1.15.0.tar.gz(r-4.7-any)SFEData_1.15.0.tar.gz(r-4.6-any)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
SFEData/json (API)

# Install 'SFEData' in R:

install.packages('SFEData', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/pachterlab/sfedata/issues

On BioConductor:SFEData-1.15.0(data/experiment 3.24)SFEData-1.14.0(data/experiment 3.23)

experimenthub expressiondata mus_musculus_data homo_sapiens_data spatialdata tissue singlecelldata datapkg

6.79 score 2 stars 1 packages 343 scripts 10 exports 57 dependencies

Last updated from:463951e6a1. Checks:1 ERROR, 3 OK. Indexed: yes.

This is a data package. Data packages may be large and do not get checked across all platforms.

Target	Result	Time
bioc-checks	ERROR	189
linux-devel	OK	350
source / vignettes	OK	245
linux-release	OK	295

Exports:BiermannMelaMetasData CosMXOutput HeNSCLCData JanesickBreastData LohoffGastrulationData McKellarMuscleData SeuratTestData VizgenLiverData VizgenOutput XeniumOutput

Dependencies:AnnotationDbi AnnotationHub askpass Biobase BiocBaseUtils BiocFileCache BiocGenerics BiocManager BiocVersion Biostrings bit bit64 blob cachem cli cpp11 crayon curl DBI dbplyr dplyr ExperimentHub fastmap filelock generics glue httr httr2 IRanges jsonlite KEGGREST lifecycle magrittr memoise mime openssl pillar pkgconfig png purrr R6 rappdirs rlang RSQLite S4Vectors Seqinfo stringi stringr sys tibble tidyr tidyselect utf8 vctrs withr XVector yaml

Example SpatialFeatureExperiment datasets

Installation | Usage

Rendered fromSFEData.Rmdusingknitr::rmarkdown

Last update: 2024-04-29
Started: 2022-07-01

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Melanoma metastasis slide-seq2 data	BiermannMelaMetasData
CosMX output from mouse brain	CosMXOutput
Nanostring FFPE CosMX human NSCLC data	HeNSCLCData
Xenium FFPE human breast cancer data	JanesickBreastData
seqFISH mouse gastrulation dataset	LohoffGastrulationData
Download McKellar et al. mouse skeletal muscle data	McKellarMuscleData
Seurat objects to test coercion function	SeuratTestData
Example SpatialFeatureExperiment datasets	SFEData-package SFEData
Vizgen MERFISH mouse liver data	VizgenLiverData
Vizgen MERFISH output from human brain cancer	VizgenOutput
Xenium output	XeniumOutput