spatialdataR
This is the development version of spatialdataR; to use it, please install the devel version of Bioconductor.
Representation of Python's spatialdata in R
Bioconductor version: Development (3.24)
R interface to Python/scverse's 'spatialdata' framework for unified spatial omics data handling. Adheres to OME-NGFF standards, providing lazy, on-disk representations for multiscale images and labels (ZarrArray), as well as points and shapes (DuckDB-backed tables). Includes handling of coordinate transformation systems and spatial utilities for cropping, masking, and querying. Integrates tabular annotations as 'SingleCellExperiment's (via 'anndataR'), enabling interoperable spatial omics workflows across R and Python.
Author: Helena L. Crowell [aut, cre] 
, Artür Manukyan [aut] , Hugo Gruson [aut] , Vince Carey [aut]
Maintainer: Helena L. Crowell <helena at crowell.eu>
citation("spatialdataR")):Helena L. Crowell, Artür Manukyan, Hugo Gruson, Vince Carey. spatialdataR: Representation of Python's spatialdata in R. doi:10.18129/B9.bioc.spatialdataR, R package version 0.99.44, https://bioconductor.org/packages/spatialdataR.
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")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("spatialdataR")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("spatialdataR")| spatialdataR | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DataImport, DataRepresentation, GeneExpression, ImmunoOncology, Infrastructure, SingleCell, Software, Spatial, Transcriptomics |
| Version | 0.99.44 |
| In Bioconductor since | BioC 3.24 (R-4.6) |
| License | Artistic-2.0 |
| Depends | R (>= 4.5) |
| Imports | anndataR (>= 1.1.3), BiocGenerics (>= 0.59.6), DBI, DelayedArray, dplyr, duckspatial, graph, Matrix, methods, Rarr, RBGL, rlang, sf, S4Vectors, SingleCellExperiment, SummarizedExperiment, SparseArray, ZarrArray |
| System Requirements | |
| URL | https://helenalc.github.io/spatialdataR https://github.com/HelenaLC/spatialdataR |
| Bug Reports | https://github.com/HelenaLC/spatialdataR/issues |
See More
| Suggests | BiocStyle, EBImage, knitr, Rgraphviz, testthat (>= 3.0.0) |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | spatialdataR_0.99.44.tar.gz |
| Windows Binary (x86_64) | spatialdataR_0.99.44.zip |
| macOS Binary (big-sur-x86_64) | spatialdataR_0.99.44.tgz |
| macOS Binary (sonoma-arm64) | spatialdataR_0.99.44.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/spatialdataR |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/spatialdataR |
| Package Short Url | https://bioconductor.org/packages/spatialdataR/ |
| Package Downloads Report | Download Stats |