Package: anndataR 0.99.0

Robrecht Cannoodt

anndataR: AnnData interoperability in R

Bring the power and flexibility of AnnData to the R ecosystem, allowing you to effortlessly manipulate and analyze 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], Data Intuitive [fnd, cph], Chan Zuckerberg Initiative [fnd]

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anndataR.pdf |anndataR.html✨
anndataR/json (API)
NEWS

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

Peer review:

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

On CRAN:

singlecelldataimportdatarepresentationanndatah5ad

7.78 score 68 stars 31 scripts 8 exports 10 dependencies

Last updated 5 days agofrom:dd38304a59. Checks:1 OK, 4 NOTE, 3 ERROR. Indexed: no.

TargetResultLatest binary
Doc / VignettesOKFeb 06 2025
R-4.5-winERRORFeb 06 2025
R-4.5-macNOTEFeb 06 2025
R-4.5-linuxNOTEFeb 06 2025
R-4.4-winNOTEFeb 06 2025
R-4.4-macNOTEFeb 06 2025
R-4.3-winERRORFeb 06 2025
R-4.3-macERRORFeb 06 2025

Exports:AnnDatafrom_Seuratfrom_SingleCellExperimentgenerate_datasetread_h5adto_Seuratto_SingleCellExperimentwrite_h5ad

Dependencies:cligluelatticelifecyclemagrittrMatrixpurrrR6rlangvctrs

Detailed look into the mapping between AnnData and SingleCellExperiment objects

Louise Deconinck

Rendered fromsinglecellexperiment_mapping.Rmdusingknitr::rmarkdownon Feb 06 2025.

Last update: 2025-02-06
Started: 2025-02-06

Development status

Rendered fromdevelopment_status.Rmdusingknitr::rmarkdownon Feb 06 2025.

Last update: 2025-01-16
Started: 2025-01-16

Known issues

Rendered fromknown_issues.Rmdusingknitr::rmarkdownon Feb 06 2025.

Last update: 2025-01-16
Started: 2025-01-16

Read/write H5AD files

Rendered fromusage_h5ad.Rmdusingknitr::rmarkdownon Feb 06 2025.

Last update: 2025-01-16
Started: 2025-01-16

Read/write Seurat objects using anndataR

Rendered fromusage_seurat.Rmdusingknitr::rmarkdownon Feb 06 2025.

Last update: 2025-01-16
Started: 2025-01-16

Read/write SingleCellExperiment objects using anndataR

Rendered fromusage_singlecellexperiment.Rmdusingknitr::rmarkdownon Feb 06 2025.

Last update: 2025-02-06
Started: 2025-01-16

Software design

Rendered fromsoftware_design.Rmdusingknitr::rmarkdownon Feb 06 2025.

Last update: 2025-01-16
Started: 2025-01-16

Using anndataR

Robrecht Cannoodt, Luke Zappia, Martin Morgan, Louise Deconinck

Rendered fromanndataR.Rmdusingknitr::rmarkdownon Feb 06 2025.

Last update: 2025-01-16
Started: 2024-11-08