This is the development version of zellkonverter; for the stable release version, see zellkonverter.

Conversion Between scRNA-seq Objects

Bioconductor version: Development (3.20)

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 lazappi.id.au>

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


To install this package, start R (version "4.4") and enter:

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

# The following initializes usage of Bioc devel


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 1.15.0
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
URL https://github.com/theislab/zellkonverter
Bug Reports https://github.com/theislab/zellkonverter/issues
See More
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_1.15.0.tar.gz
Windows Binary zellkonverter_1.15.0.zip
macOS Binary (x86_64) zellkonverter_1.15.0.tgz
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/zellkonverter
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/zellkonverter
Bioc Package Browser https://code.bioconductor.org/browse/zellkonverter/
Package Short Url https://bioconductor.org/packages/zellkonverter/
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