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Conversion Between scRNA-seq Objects

Bioconductor version: Release (3.18)

Provides methods to convert between Python AnnData objects and SingleCellExperiment objects. These are primarily intended for use by downstream Bioconductor packages that wrap Python methods for single-cell data analysis. It also includes functions to read and write H5AD files used for saving AnnData objects to disk.

Author: Luke Zappia [aut, cre] , Aaron Lun [aut] , Jack Kamm [ctb] , Robrecht Cannoodt [ctb] (, rcannood)

Maintainer: Luke Zappia <luke at>

Citation (from within R, enter citation("zellkonverter")):


To install this package, start R (version "4.3") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

Converting to/from AnnData to SingleCellExperiments HTML R Script
Reference Manual PDF


biocViews DataImport, DataRepresentation, SingleCell, Software
Version 1.12.1
In Bioconductor since BioC 3.12 (R-4.0) (3.5 years)
License MIT + file LICENSE
Imports Matrix, basilisk, reticulate, SingleCellExperiment(>= 1.11.6), SummarizedExperiment, DelayedArray, methods, S4Vectors, utils, cli
System Requirements
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Suggests anndata, BiocFileCache, BiocStyle, covr, HDF5Array, knitr, pkgload, rmarkdown, rhdf5(>= 2.45.1), scRNAseq, spelling, testthat, withr
Linking To
Depends On Me OSCA.intro
Imports Me singleCellTK, velociraptor
Suggests Me cellxgenedp, CuratedAtlasQueryR, GloScope, HCATonsilData, HDF5Array
Links To Me
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package zellkonverter_1.12.1.tar.gz
Windows Binary (64-bit only)
macOS Binary (x86_64) zellkonverter_1.12.1.tgz
macOS Binary (arm64)
Source Repository git clone
Source Repository (Developer Access) git clone
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