Package: zellkonverter 1.17.0

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]

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zellkonverter.pdf |zellkonverter.html✨
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-1.17.0(bioc 3.21)zellkonverter-1.16.0(bioc 3.20)

singlecell dataimport datarepresentation bioconductor conversion scrna-seq

11.07 score 157 stars 4 packages 632 scripts 2.4k downloads 8 exports 43 dependencies

Last updated 2 months agofrom:5381a5a319. Checks:1 OK, 6 NOTE. Indexed: yes.

Target	Result	Latest binary
Doc / Vignettes	OK	Jan 21 2025
R-4.5-win	NOTE	Jan 21 2025
R-4.5-linux	NOTE	Jan 21 2025
R-4.4-win	NOTE	Jan 21 2025
R-4.4-mac	NOTE	Jan 21 2025
R-4.3-win	NOTE	Jan 21 2025
R-4.3-mac	NOTE	Jan 21 2025

Exports:.AnnDataVersions AnnData2SCE AnnDataDependencies readH5AD SCE2AnnData setZellkonverterVerbose writeH5AD zellkonverterAnnDataEnv

Dependencies:abind askpass basilisk basilisk.utils Biobase BiocGenerics cli crayon curl DelayedArray dir.expiry filelock generics GenomeInfoDb GenomeInfoDbData GenomicRanges here httr IRanges jsonlite lattice Matrix MatrixGenerics matrixStats mime openssl png R6 rappdirs Rcpp RcppTOML reticulate rlang rprojroot S4Arrays S4Vectors SingleCellExperiment SparseArray SummarizedExperiment sys UCSC.utils withr XVector

Converting single-cell data structures between Bioconductor and Python

Luke Zappia, Aaron Lun

Rendered fromzellkonverter.Rmdusingknitr::rmarkdownon Jan 21 2025.

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

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
zellkonverter: Conversion Between scRNA-seq Objects	zellkonverter-package zellkonverter
Convert between AnnData and SingleCellExperiment	AnnData-Conversion AnnData2SCE SCE2AnnData
AnnData environment	.AnnDataVersions AnnData-Environment AnnDataDependencies zellkonverterAnnDataEnv
Expect SCE	expectSCE
Convert between Python and R objects	py_to_r.numpy.ndarray r-py-conversion
Read H5AD	readH5AD
Set zellkonverter verbose	setZellkonverterVerbose
Validate H5AD SCE	validateH5ADSCE
Write H5AD	writeH5AD