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
anndataR_1.3.0.zip(r-4.7)anndataR_1.3.0.zip(r-4.6)anndataR_1.3.0.zip(r-4.5)
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✨
DESCRIPTION |NEWS
card.svg |card.png
anndataR/json (API)

# Install 'anndataR' in R:
install.packages('anndataR', repos = c('https://lazappi.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

11.58 score 188 stars 3 packages 302 scripts 9 exports 19 dependencies

Last updated from:07612e4f0e. Checks:7 NOTE, 2 OK. Indexed: no.

TargetResultTimeFilesSyslog
linux-devel-x86_64NOTE648
source / vignettesOK341
linux-release-x86_64NOTE656
macos-release-arm64NOTE367
macos-oldrel-arm64NOTE490
windows-develNOTE805
windows-releaseNOTE740
windows-oldrelNOTE834
wasm-releaseOK162

Exports:AnnDataAnnDataViewas_AnnDatagenerate_datasetget_generator_typesread_h5adread_zarrwrite_h5adwrite_zarr

Dependencies:cliglueherejsonlitelatticelifecyclemagrittrMatrixpngpurrrR6rappdirsRcppRcppTOMLreticulaterlangrprojrootvctrswithr

Read/write Seurat objects using anndataR
Introduction | Prerequisites | Reading H5AD files and Zarr stores to a Seurat Object | Mapping between AnnData and Seurat | Writing a Seurat object to a H5AD file or Zarr store | Session info
Rendered fromusage_seurat.Rmdusingknitr::rmarkdown

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

Read/write SingleCellExperiment objects using anndataR
Introduction | Prerequisites | Reading H5AD files and Zarr stores to a SingleCellExperiment object | Mapping between AnnData and SingleCellExperiment | Writing a SingleCellExperiment object to a H5AD file or Zarr store | Session info
Rendered fromusage_singlecellexperiment.Rmdusingknitr::rmarkdown

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

Using anndataR
Introduction | Relationship to other packages | Installation | Usage | Read from disk | Using AnnData objects | Interoperability | Manually create an AnnData object | Write to disk | Subsetting AnnData objects | Basic subsetting | Combined subsetting | Using different index types | Working with views | Citing anndataR | Session info
Rendered fromanndataR.Rmdusingknitr::rmarkdown

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

Python Integration with anndataR
Introduction | Prerequisites | Basic Integration with scanpy | Conversion to R objects | Multi-modal data with mudata | Session info | R | Python
Rendered fromusage_python.Rmdusingknitr::rmarkdown

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

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