Package: anndata 0.9.0
Robrecht Cannoodt
anndata: 'anndata' for R (Superseded)
A 'reticulate' wrapper for the Python package 'anndata'. Provides a scalable way of keeping track of data and learned annotations. Used to read from and write to the h5ad file format. This package is superseded by 'anndataR' <https://anndataR.scverse.org>, which provides native R backends for the 'AnnData' data structure, along with conversion to/from 'SingleCellExperiment' and 'Seurat' objects.
Authors:
anndata_0.9.0.tar.gz
anndata_0.9.0.zip(r-4.7)anndata_0.9.0.zip(r-4.6)anndata_0.9.0.zip(r-4.5)
anndata_0.9.0.tgz(r-4.6-any)anndata_0.9.0.tgz(r-4.5-any)
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anndata_0.9.0.tgz(r-4.5-emscripten)
anndata.pdf |anndata.html✨
anndata/json (API)
NEWS
| # Install 'anndata' in R: |
| install.packages('anndata', repos = c('https://dynverse.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/dynverse/anndata/issues
Pkgdown/docs site:https://anndata.dynverse.org
Last updated from:1da726718b. Checks:5 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| source / vignettes | OK | 204 | ||
| macos-oldrel-arm64 | OK | 88 | ||
| windows-release | OK | 95 | ||
| windows-oldrel | OK | 111 | ||
| wasm-release | OK | 120 |
Exports:AnnDataAnnDataR6concatinstall_anndataLayersLayersR6RawRawR6read_csvread_excelread_h5adread_hdfread_loomread_mtxread_textread_umi_toolsread_zarrwrite_csvswrite_h5adwrite_loomwrite_zarr
Dependencies:assertthatcliherejsonlitelatticelifecycleMatrixpngR6rappdirsRcppRcppTOMLreticulaterlangrprojrootwithr
Demo with scanpy
Rendered fromscanpy_demo.Rmdusingknitr::rmarkdownon Apr 01 2026.Last update: 2025-06-03
Started: 2021-03-28
Getting started
Rendered fromgetting_started.Rmdusingknitr::rmarkdownon Apr 01 2026.Last update: 2025-06-03
Started: 2021-03-28
Migrating from anndata to anndataR
Rendered frommigration_to_anndataR.Rmdusingknitr::rmarkdownon Apr 01 2026.Last update: 2026-04-01
Started: 2026-04-01
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| anndata - Annotated Data | anndata-package anndata |
| Test if two objects objects are equal | all.equal.AnnDataR6 all.equal.LayersR6 all.equal.RawR6 |
| Create an Annotated Data Matrix | AnnData AnnDataR6 |
| concat | concat |
| AnnData Helpers | as.data.frame.AnnDataR6 as.matrix.AnnDataR6 dim.AnnDataR6 dimnames.AnnDataR6 dimnames<-.AnnDataR6 py_to_r.anndata._core.anndata.AnnData py_to_r.anndata._core.sparse_dataset.SparseDataset py_to_r.h5py._hl.dataset.Dataset r_to_py.AnnDataR6 t.AnnDataR6 [.AnnDataR6 |
| Raw Helpers | as.matrix.RawR6 dim.RawR6 dimnames.RawR6 py_to_r.anndata._core.raw.Raw r_to_py.RawR6 [.RawR6 |
| Install anndata | install_anndata |
| Create a Layers object | Layers LayersR6 |
| Layers Helpers | length.LayersR6 names.LayersR6 py_to_r.anndata._core.aligned_mapping.LayersBase r_to_py.LayersR6 [.LayersR6 [<-.LayersR6 [[.LayersR6 [[<-.LayersR6 |
| Convert between Python and R objects | names.collections.abc.Mapping py_to_r.anndata.abc._AbstractCSDataset py_to_r.collections.abc.KeysView py_to_r.collections.abc.Mapping py_to_r.collections.abc.Set py_to_r.pandas.core.indexes.base.Index r-py-conversion [.collections.abc.Mapping [<-.collections.abc.MutableMapping [[.collections.abc.Mapping [[<-.collections.abc.MutableMapping |
| Create a Raw object | Raw RawR6 |
| read_csv | read_csv |
| read_excel | read_excel |
| read_h5ad | read_h5ad |
| read_hdf | read_hdf |
| read_loom | read_loom |
| read_mtx | read_mtx |
| read_text | read_text |
| read_umi_tools | read_umi_tools |
| Read from a hierarchical Zarr array store. | read_zarr |
| Write annotation to .csv files. | write_csvs |
| Write .h5ad-formatted hdf5 file. | write_h5ad |
| Write .loom-formatted hdf5 file. | write_loom |
| Write a hierarchical Zarr array store. | write_zarr |
