anndataR
AnnData interoperability in R
Bioconductor version: 3.24 · Package version: 1.3.2
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
Bring the power and flexibility of AnnData to the R ecosystem, allowing you to effortlessly manipulate and analyse your single-cell data. This package lets you work with backed h5ad and zarr files, directly access various slots (e.g. X, obs, var), or convert the data into SingleCellExperiment and Seurat objects.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("anndataR")Details
| Maintainer | Robrecht Cannoodt <rcannood@gmail.com> |
| Author | Robrecht Cannoodt [aut, cre] (ORCID: <https://orcid.org/0000-0003-3641-729X>, github: rcannood), Luke Zappia [aut] (ORCID: <https://orcid.org/0000-0001-7744-8565>, github: lazappi), Martin Morgan [aut] (ORCID: <https://orcid.org/0000-0002-5874-8148>, github: mtmorgan), Louise Deconinck [aut] (ORCID: <https://orcid.org/0000-0001-8100-6823>, github: LouiseDck), Danila Bredikhin [ctb] (ORCID: <https://orcid.org/0000-0001-8089-6983>, github: gtca), Isaac Virshup [ctb] (ORCID: <https://orcid.org/0000-0002-1710-8945>, github: ivirshup), Brian Schilder [ctb] (ORCID: <https://orcid.org/0000-0001-5949-2191>, github: bschilder), Chananchida Sang-aram [ctb] (ORCID: <https://orcid.org/0000-0002-0922-0822>, github: csangara), Artür Manukyan [ctb] (ORCID: <https://orcid.org/0000-0002-0441-9517>, github: Artur-man), Hugo Gruson [ctb] (ORCID: <https://orcid.org/0000-0002-4094-1476>, github: Bisaloo), Data Intuitive [fnd], Chan Zuckerberg Initiative [fnd], scverse consortium [spn] |
| License | MIT + file LICENSE |
| URL | https://anndataR.scverse.org/, https://github.com/scverse/anndataR |
| Bug Reports | https://github.com/scverse/anndataR/issues |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | DataImport, DataRepresentation, SingleCell, Software |
| Package Short Url | https://bioconductor.org/packages/anndataR/ |
Citation
From within R, enter citation("anndataR"):
Robrecht Cannoodt, Luke Zappia, Martin Morgan, Louise Deconinck. anndataR: AnnData interoperability in R. doi:10.18129/B9.bioc.anndataR, R package version 1.3.2, https://bioconductor.org/packages/anndataR.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
- Python Integration with anndataR
- Read/write Seurat objects using anndataR
- Read/write SingleCellExperiment objects using anndataR
- Using anndataR
Download
Follow the installation instructions to use this package in your R session.
| Source package | anndataR_1.3.2.tar.gz |
| Windows binary (x86_64) | anndataR_1.3.2.zip |
| macOS binary (arm64) | anndataR_1.3.2.tgz |
| macOS binary (x86_64) | anndataR_1.3.2.tgz |
Dependencies
Depends: R (>= 4.5.0)
Imports: cli, lifecycle, Matrix, methods, purrr, R6 (>= 2.4.0), reticulate (>= 1.41.1), rlang, stats
Suggests: BiocFileCache, BiocStyle, DelayedArray, HDF5Array, jsonlite, knitr, processx, rhdf5 (>= 2.57.5), Rarr (>= 2.1.13), rmarkdown, S4Vectors, Seurat, SeuratObject, SingleCellExperiment, spelling, SummarizedExperiment, testthat (>= 3.0.0), vctrs, withr, yaml
Reverse dependencies
Imports Me (2): cellNexus, spatialdataR
Suggests Me (8): dyngen, GEOquery, HistoImagePlot, imageFeatureTCGA, imageTCGAutils, savingBiocObjects, SpaceMarkers, ZarrArray