Package: anndataR 1.3.0

Robrecht Cannoodt

anndataR: AnnData interoperability in R

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.

Authors:Robrecht Cannoodt [aut, cre], Luke Zappia [aut], Martin Morgan [aut], Louise Deconinck [aut], Danila Bredikhin [ctb], Isaac Virshup [ctb], Brian Schilder [ctb], Chananchida Sang-aram [ctb], Artür Manukyan [ctb], Hugo Gruson [ctb], Data Intuitive [fnd], Chan Zuckerberg Initiative [fnd], scverse consortium [spn]

anndataR_1.3.0.tar.gz
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anndataR_1.3.0.tgz(r-4.6-any)anndataR_1.3.0.tgz(r-4.5-any)
anndataR_1.3.0.tar.gz(r-4.7-any)anndataR_1.3.0.tar.gz(r-4.6-any)
anndataR_1.3.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
anndataR/json (API)
NEWS

# Install 'anndataR' in R:
install.packages('anndataR', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/scverse/anndatar/issues

Pkgdown/docs site:https://anndatar.scverse.org

On BioConductor:anndataR-1.3.0(bioc 3.24)anndataR-1.2.0(bioc 3.23)

singlecelldataimportdatarepresentationanndatah5adinteroperability

10.89 score 181 stars 1 packages 172 scripts 1.3k downloads 9 exports 19 dependencies

Last updated from:a460e0597e. Checks:1 WARNING, 7 ERROR, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksWARNING197
linux-devel-x86_64ERROR758
source / vignettesOK363
linux-release-x86_64ERROR828
macos-release-arm64ERROR619
macos-oldrel-arm64ERROR485
windows-develERROR907
windows-releaseERROR1056
windows-oldrelERROR881
wasm-releaseOK167

Exports:AnnDataAnnDataViewas_AnnDatagenerate_datasetget_generator_typesread_h5adread_zarrwrite_h5adwrite_zarr

Dependencies:cliglueherejsonlitelatticelifecyclemagrittrMatrixpngpurrrR6rappdirsRcppRcppTOMLreticulaterlangrprojrootvctrswithr

Python Integration with anndataR

Rendered fromusage_python.Rmdusingknitr::rmarkdownon May 29 2026.

Last update: 2026-02-24
Started: 2025-09-24

Read/write Seurat objects using anndataR

Rendered fromusage_seurat.Rmdusingknitr::rmarkdownon May 29 2026.

Last update: 2026-04-24
Started: 2025-01-16

Read/write SingleCellExperiment objects using anndataR

Rendered fromusage_singlecellexperiment.Rmdusingknitr::rmarkdownon May 29 2026.

Last update: 2026-04-24
Started: 2025-01-16

Using anndataR

Robrecht Cannoodt, Luke Zappia, Martin Morgan, Louise Deconinck

Rendered fromanndataR.Rmdusingknitr::rmarkdownon May 29 2026.

Last update: 2026-04-24
Started: 2024-11-08

Readme and manuals

Help Manual

Help pageTopics
Abstract AnnData classAbstractAnnData
S3 Methods for AbstractAnnData ObjectsAbstractAnnData-s3methods dim.AbstractAnnData dimnames.AbstractAnnData dimnames<-.AbstractAnnData ncol.AbstractAnnData nrow.AbstractAnnData [.AbstractAnnData
Create an in-memory AnnData object.AnnData
AnnData structure and usageAnnData-usage
A View of an AnnData ObjectAnnDataView
Convert to an 'AnnData' objectas_AnnData as_AnnData.Seurat as_AnnData.SingleCellExperiment
Convert an 'AnnData' to a 'Seurat'as_Seurat
Convert an 'AnnData' to a 'SingleCellExperiment'as_SingleCellExperiment
Generate a mock datasetgenerate_dataset get_generator_types
HDF5AnnDataHDF5AnnData
InMemoryAnnDataInMemoryAnnData
Read H5ADread_h5ad
Read Zarrread_zarr
Reticulate Helper Functions for AnnData Conversionpy_to_r.anndata._core.anndata.AnnData py_to_r.collections.abc.Mapping reticulate-helpers r_to_py.AbstractAnnData
ReticulateAnnDataReticulateAnnData
Write H5ADwrite_h5ad
Write Zarrwrite_zarr
ZarrAnnDataZarrAnnData