Package 'SpatialData.data'

SD.data_available

Description

Function for interrogating files across buckets. Please use paws.storage::s3' to interrogate buckets for zipped zarr archives or raw readouts for various platforms.

Usage

SD.data_available(src = "sandbox")

Arguments

src	The name of the query bucket. biocOSN Bioc's Open Storage Network (NSF) OSN bucket (spatialdata v0.3.0, zarr v2) sandbox scverse's spatialdata-sandbox bucket at EMBL.

Value

a vector of example (zipped) SpatialData stores available at source

Examples

Sys.setenv(AWS_REGION = "us-east-1")
library(paws.storage)
 
SD.data_available()
SD.data_available("sandbox")
SD.data_available("biocOSN")

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SD.data_list

Description

Returns metadata of available data from Bioc OSN and scverse spatialdata- sandbox S3 buckets

Usage

SD.data_list(metadata = FALSE)

Arguments

metadata

if TRUE, all columns will be returned, e.g. File size, License etc.

Value

a vector of dataset names or a data.frame

Examples

SD.data_list()
SD.data_list(metadata = TRUE)

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retrieve scverse-curated 'SpatialData' .zarr archive

Description

This function consolidates the retrieval and caching and transformation of scverse-curated Zarr archives and 10x-curated Xenium archives.

Usage

SD.data_load(id, target = tempfile(), src)

Arguments

id	character string; dataset identifier
target	character(1), defaults to tempfile(); use a different value if you wish to retain the unzipped .zarr store persistently.
src	The name of the source, i.e. query bucket. biocOSN Bioc's Open Storage Network (NSF) OSN bucket (spatialdata v0.3.0, zarr v2) sandbox scverse's spatialdata-sandbox bucket at EMBL.

Details

• MouseIntestineVisHD: Visium HD 3.0.0 (10x Genomics) dataset of mouse intestine; source (biocOSN): https://www.10xgenomics.com/datasets/visium-hd-cytassist-gene-expression-libraries-of-mouse-intestine

• MouseBrainVisHD: Visium HD 4.0.1 (10x Genomics) dataset of mouse brain; source (sandbox): https://www.10xgenomics.com/datasets/visium-hd-three-prime-mouse-brain-fresh-frozen

• MouseBrainVis: Visium (10x Genomics) dataset of mouse brain; source (sandbox): https://www.ebi.ac.uk/biostudies/arrayexpress/studies/E-MTAB-11114

• LungAdenocarcinomaMCMICRO: MCMICRO dataset of human small cell lung adenocarcinoma; source (biocOSN)

• MouseBrainMERFISH: MERFISH dataset of mouse brain tissue; source (biocOSN)

• MouseLiverMERFISH: MERFISH dataset of mouse liver tissue (SPArrOW output); source (sandbox): https://www.biorxiv.org/content/10.1101/2024.07.04.601829v1

• MulticancerSteinbock: imaging mass cytometry dataset of four cancers; source (biocOSN): https://www.nature.com/articles/s41596-023-00881-0

• ColorectalCarcinomaMIBITOF: MIBI-TOF dataset of colorectal carcinoma; source (biocOSN)

• JanesickBreastVisiumEnh: Visium (10x Genomics) dataset of breast cancer; source (biocOSN): https://www.nature.com/articles/s41467-023-43458-x

• JanesickBreastXeniumRep1: first of two Xenium (10x Genomics) sections associated with the Visium section from Janesick et al.; source (biocOSN)

• JanesickBreastXeniumRep2: second of two Xenium (10x Genomics) sections associated with the Visium section from Janesick et al.; source (biocOSN)

• HumanLungMulti_10x: Xenium (10x Genomics) data on lung cancer; source (biocOSN): https://www.10xgenomics.com/datasets/preview-data-ffpe-human-lung-cancer-with-xenium-multimodal-cell-segmentation-1-standard

• SpaceMHelaniH3T3: SpaceM on Hepa and NIH3T3 cells; source (sandbox); more info: https://github.com/giovp/spatialdata-sandbox/blob/main/spacem_helanih3t3/README.md

Value

an instance of SpatialData, or throws an error if the dataset identifier (id)does not uniquely match the name of any resource, see SD.data_list for the list of datasets.

Examples

Sys.setenv(AWS_REGION = "us-east-1")

# load using `SD.data_load`
ld <- SD.data_load("ColorectalCarcinomaMIBITOF")
ld

# load data from biocOSN source (Zarr v2)
ld <- SD.data_load("ColorectalCarcinomaMIBITOF", src = "biocOSN")

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