Package: zellkonverter 1.23.0

Luke Zappia

zellkonverter: Conversion Between scRNA-seq Objects

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.

Authors:Luke Zappia [aut, cre], Aaron Lun [aut], Jack Kamm [ctb], Robrecht Cannoodt [ctb], Gabriel Hoffman [ctb], Marek Cmero [ctb]

zellkonverter_1.23.0.tar.gz
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zellkonverter_1.23.0.tgz(r-4.6-any)zellkonverter_1.23.0.tgz(r-4.5-any)
zellkonverter_1.23.0.tar.gz(r-4.7-any)zellkonverter_1.23.0.tar.gz(r-4.6-any)
zellkonverter_1.23.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
zellkonverter/json (API)
NEWS

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

Bug tracker:https://github.com/theislab/zellkonverter/issues

On BioConductor:zellkonverter-1.23.0(bioc 3.24)zellkonverter-1.22.0(bioc 3.23)

singlecelldataimportdatarepresentationbioconductorconversionscrna-seq

12.02 score 210 stars 6 packages 1.4k scripts 4.0k downloads 8 exports 32 dependencies

Last updated from:3cbe1b2dde. Checks:4 NOTE, 2 OK, 1 FAIL, 3 ERROR. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksNOTE232
linux-devel-x86_64NOTE3843
source / vignettesOK1218
linux-release-x86_64FAIL3934
macos-release-arm64NOTE2890
macos-oldrel-arm64NOTE3497
windows-develERROR1023
windows-releaseERROR1008
windows-oldrelERROR1031
wasm-releaseOK201

Exports:.AnnDataVersionsAnnData2SCEAnnDataDependenciesreadH5ADSCE2AnnDatasetZellkonverterVerbosewriteH5ADzellkonverterAnnDataEnv

Dependencies:abindbasiliskBiobaseBiocGenericscliDelayedArraydir.expiryfilelockgenericsGenomicRangeshereIRangesjsonlitelatticeMatrixMatrixGenericsmatrixStatspngrappdirsRcppRcppTOMLreticulaterlangrprojrootS4ArraysS4VectorsSeqinfoSingleCellExperimentSparseArraySummarizedExperimentwithrXVector

Converting single-cell data structures between Bioconductor and Python

Luke Zappia, Aaron Lun

Rendered fromzellkonverter.Rmdusingknitr::rmarkdownon Jun 04 2026.

Last update: 2024-10-18
Started: 2020-06-15

Readme and manuals

Help Manual

Help pageTopics
zellkonverter: Conversion Between scRNA-seq Objectszellkonverter-package zellkonverter
Convert between AnnData and SingleCellExperimentAnnData-Conversion AnnData2SCE SCE2AnnData
AnnData environment.AnnDataVersions AnnData-Environment AnnDataDependencies zellkonverterAnnDataEnv
Expect SCEexpectSCE
Convert between Python and R objectspy_to_r.numpy.ndarray r-py-conversion
Read H5ADreadH5AD
Set zellkonverter verbosesetZellkonverterVerbose
Validate H5AD SCEvalidateH5ADSCE
Write H5ADwriteH5AD