Package: zellkonverter 1.15.1

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]

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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-1.15.0(bioc 3.20)zellkonverter-1.14.0(bioc 3.19)

bioconductor-package

8 exports 1.95 score 43 dependencies 2 dependents

Last updated 19 days agofrom:328e7ea895

Exports:.AnnDataVersions AnnData2SCE AnnDataDependencies readH5AD SCE2AnnData setZellkonverterVerbose writeH5AD zellkonverterAnnDataEnv

Dependencies:abind askpass basilisk basilisk.utils Biobase BiocGenerics cli crayon curl DelayedArray dir.expiry filelock 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 zlibbioc

Converting single-cell data structures between Bioconductor and Python

Luke Zappia, Aaron Lun

Rendered fromzellkonverter.Rmdusingknitr::rmarkdownon Jun 24 2024.

Last update: 2022-04-17
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