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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
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 |
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 (>= 4.6) |
| 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 |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
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) | |
| macOS Binary (big-sur-x86_64) | spatialdataR_0.99.44.tgz |
| macOS Binary (sonoma-arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/spatialdataR |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/spatialdataR |
| Bioc Package Browser | https://code.bioconductor.org/browse/spatialdataR/ |
| Package Short Url | https://bioconductor.org/packages/spatialdataR/ |
| Package Downloads Report | Download Stats |