anndataR

This is the released version of anndataR; for the devel version, see anndataR.

All versions

AnnData interoperability in R

Bioconductor version: Release (3.23)

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.

Author: Robrecht Cannoodt [aut, cre] (ORCID: ORCID: 0000-0003-3641-729X , github: rcannood), Luke Zappia [aut] (ORCID: ORCID: 0000-0001-7744-8565 , github: lazappi), Martin Morgan [aut] (ORCID: ORCID: 0000-0002-5874-8148 , github: mtmorgan), Louise Deconinck [aut] (ORCID: ORCID: 0000-0001-8100-6823 , github: LouiseDck), Danila Bredikhin [ctb] (ORCID: ORCID: 0000-0001-8089-6983 , github: gtca), Isaac Virshup [ctb] (ORCID: ORCID: 0000-0002-1710-8945 , github: ivirshup), Brian Schilder [ctb] (ORCID: ORCID: 0000-0001-5949-2191 , github: bschilder), Chananchida Sang-aram [ctb] (ORCID: ORCID: 0000-0002-0922-0822 , github: csangara), Artür Manukyan [ctb] (ORCID: ORCID: 0000-0002-0441-9517 , github: Artur-man), Hugo Gruson [ctb] (ORCID: ORCID: 0000-0002-4094-1476 , github: Bisaloo), Data Intuitive [fnd], Chan Zuckerberg Initiative [fnd], scverse consortium [spn]

Maintainer: Robrecht Cannoodt <rcannood at gmail.com>

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 1.2.2, https://bioconductor.org/packages/anndataR.

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")

BiocManager::install("anndataR")

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("anndataR")

Using anndataR to read and convert	HTML	R Script
Python integration with anndataR	HTML	R Script
Read/write Seurat objects using anndataR	HTML	R Script
Read/write SingleCellExperiment objects using anndataR	HTML	R Script
Reference Manual	PDF
NEWS	Text
LICENSE	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DataImport, DataRepresentation, SingleCell, Software
Version	1.2.2
In Bioconductor since	BioC 3.22 (R-4.5) (1 year)
License	MIT + file LICENSE
Depends	R (>= 4.5.0)
Imports	cli, lifecycle, Matrix, methods, purrr, R6 (>= 2.4.0), reticulate (>= 1.41.1), rlang, stats
System Requirements
URL	https://anndataR.scverse.org/ https://github.com/scverse/anndataR
Bug Reports	https://github.com/scverse/anndataR/issues

Suggests	BiocFileCache, BiocStyle, knitr, processx, rhdf5 (>= 2.52.1), Rarr (>= 1.11.12), rmarkdown, S4Vectors, Seurat, SeuratObject, SingleCellExperiment, spelling, SummarizedExperiment, testthat (>= 3.0.0), vctrs, withr, yaml
Linking To
Enhances
Depends On Me
Imports Me	OSTA
Suggests Me	dyngen, HistoImagePlot, imageFeatureTCGA, imageTCGAutils
Links To Me
Build Report	Build Report, r-universe

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	anndataR_1.2.2.tar.gz
Windows Binary (x86_64)	anndataR_1.2.2.zip
macOS Binary (big-sur-x86_64)	anndataR_1.2.2.tgz
macOS Binary (sonoma-arm64)	anndataR_1.2.2.tgz
Source Repository	git clone https://git.bioconductor.org/packages/anndataR
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/anndataR
Package Short Url	https://bioconductor.org/packages/anndataR/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.23	Source Archive