Package: alabaster.spatial 1.12.0

Aaron Lun

alabaster.spatial: Save and Load Spatial 'Omics Data to/from File

Save SpatialExperiment objects and their images into file artifacts, and load them back into memory. This is a more portable alternative to serialization of such objects into RDS files. Each artifact is associated with metadata for further interpretation; downstream applications can enrich this metadata with context-specific properties.

Authors:Aaron Lun [aut, cre]

alabaster.spatial_1.12.0.tar.gz
alabaster.spatial_1.12.0.zip(r-4.7)alabaster.spatial_1.12.0.zip(r-4.6)alabaster.spatial_1.12.0.zip(r-4.5)
alabaster.spatial_1.12.0.tgz(r-4.6-any)alabaster.spatial_1.12.0.tgz(r-4.5-any)
alabaster.spatial_1.12.0.tar.gz(r-4.7-any)alabaster.spatial_1.12.0.tar.gz(r-4.6-any)
alabaster.spatial_1.12.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
alabaster.spatial/json (API)
NEWS

# Install 'alabaster.spatial' in R:

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

On BioConductor:alabaster.spatial-1.13.0(bioc 3.24)alabaster.spatial-1.12.0(bioc 3.23)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

dataimport datarepresentation

5.00 score 2 packages 11 scripts 299 downloads 5 exports 75 dependencies

Last updated from:c33527b91d (on RELEASE_3_23). Checks:8 NOTE, 2 OK. Indexed: no.

Target	Result	Time
bioc-checks	NOTE	205
linux-devel-x86_64	NOTE	357
source / vignettes	OK	281
linux-release-x86_64	NOTE	384
macos-release-arm64	NOTE	246
macos-oldrel-arm64	NOTE	185
windows-devel	NOTE	272
windows-release	NOTE	288
windows-oldrel	NOTE	288
wasm-release	OK	161

Exports:loadSpatialExperiment loadSpatialImage readSpatialExperiment saveObject stageObject

Dependencies:abind alabaster.base alabaster.matrix alabaster.ranges alabaster.sce alabaster.schemas alabaster.se askpass assorthead Biobase BiocFileCache BiocGenerics biocmake bit bit64 blob cachem cli cpp11 curl DBI dbplyr DelayedArray dir.expiry dplyr fastmap filelock generics GenomicRanges glue h5mread HDF5Array httr2 IRanges jsonlite jsonvalidate lattice lifecycle magick magrittr Matrix MatrixGenerics matrixStats memoise openssl pillar pkgconfig purrr R6 rappdirs Rcpp rhdf5 rhdf5filters Rhdf5lib rjson rlang RSQLite S4Arrays S4Vectors Seqinfo SingleCellExperiment SparseArray SpatialExperiment stringi stringr SummarizedExperiment sys tibble tidyr tidyselect utf8 V8 vctrs withr XVector

Save/load spatial omics data to/from file

Aaron Lun

Rendered fromuserguide.Rmdusingknitr::rmarkdownon May 29 2026.

Last update: 2024-10-16
Started: 2022-09-21

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Load a spatial image	loadSpatialImage
Read a SpatialExperiment from disk	loadSpatialExperiment readSpatialExperiment
Save a spatial experiment	saveObject,SpatialExperiment-method stageObject,SpatialExperiment-method
Stage images for upload	stageObject,RemoteSpatialImage-method stageObject,StoredSpatialImage-method stageObject,VirtualSpatialImage-method stageSpatialImage