spatialdataR
Representation of Python's spatialdata in R
Bioconductor version: 3.24 · Package version: 0.99.44
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("spatialdataR")Details
| Maintainer | Helena L. Crowell <helena@crowell.eu> |
| Author | Helena L. Crowell [aut, cre] (ORCID: <https://orcid.org/0000-0002-4801-1767>), Artür Manukyan [aut] (ORCID: <https://orcid.org/0000-0002-0441-9517>), Hugo Gruson [aut] (ORCID: <https://orcid.org/0000-0002-4094-1476>), Vince Carey [aut] (ORCID: <https://orcid.org/0000-0003-4046-0063>) |
| License | Artistic-2.0 |
| URL | https://helenalc.github.io/spatialdataR, https://github.com/HelenaLC/spatialdataR |
| Bug Reports | https://github.com/HelenaLC/spatialdataR/issues |
| Downloads rank | 1 |
| Source branch | devel |
| biocViews | DataImport, DataRepresentation, GeneExpression, ImmunoOncology, Infrastructure, SingleCell, Software, Spatial, Transcriptomics |
Documentation
Download
Follow the 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 (arm64) | spatialdataR_0.99.44.tgz |
| macOS binary (x86_64) | spatialdataR_0.99.44.tgz |
Dependencies
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