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anndata for R

⚠️ This package is superseded by anndataR.

anndataR provides a pure R implementation of the AnnData data structure with no Python required. It reads and writes .h5ad files natively and supports conversion to/from SingleCellExperiment and Seurat objects. New users should install anndataR from Bioconductor instead:

BiocManager::install("anndataR")

Existing users of anndata can follow the migration guide for guidance on switching to anndataR.

anndata for R is a reticulate wrapper for the Python anndata package.

Installation

Note: New projects should use anndataR instead. See the migration guide.

You can install anndata for R from CRAN as follows:

install.packages("anndata")

Normally, reticulate should take care of installing Miniconda and the Python anndata.

If not, try running:

reticulate::install_miniconda()
anndata::install_anndata()

Getting started

The API of anndata for R is very similar to its Python counterpart. Here is an example:

library(anndata)

ad <- read_h5ad("example_formats/pbmc_1k_protein_v3_processed.h5ad")

ad
## AnnData object with n_obs × n_vars = 713 × 33538
##     var: 'gene_ids', 'feature_types', 'genome', 'highly_variable', 'means', 'dispersions', 'dispersions_norm'
##     uns: 'hvgParameters', 'normalizationParameters', 'pca', 'pcaParameters'
##     obsm: 'X_pca'
##     varm: 'PCs'
Matrix::rowMeans(ad$X[1:10, ])
## AAACCCAAGTGGTCAG-1 AAAGGTATCAACTACG-1 AAAGTCCAGCGTGTCC-1 AACACACTCAAGAGTA-1 
##         0.06499579         0.06385104         0.06102355         0.06739055 
## AACACACTCGACGAGA-1 AACAGGGCAGGAGGTT-1 AACAGGGCAGTGTATC-1 AACAGGGTCAGAATAG-1 
##         0.08891241         0.08648681         0.09318970         0.09140243 
## AACCTGAAGATGGTCG-1 AACGGGATCGTTATCT-1 
##         0.06664118         0.07866523

See ?anndata for a full list of the functions provided by this package. Check out any of the other vignettes by clicking any of the links below:

Future work

This package is no longer under active development as it has been superseded by anndataR. Bug fixes may still be applied, but no new features are planned.

References