zellkonverter

This package is for version 3.20 of Bioconductor; for the stable, up-to-date release version, see zellkonverter.

Conversion Between scRNA-seq Objects

Bioconductor version: 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] ORCID iD ORCID: 0000-0001-7744-8565 , Aaron Lun [aut] ORCID iD ORCID: 0000-0002-3564-4813 , Jack Kamm [ctb] ORCID iD ORCID: 0000-0003-2412-756X , Robrecht Cannoodt [ctb] ( ORCID iD ORCID: 0000-0003-3641-729X , rcannood), Gabriel Hoffman [ctb] ( ORCID iD ORCID: 0000-0002-0957-0224 , GabrielHoffman)

Maintainer: Luke Zappia <luke at lazappi.id.au>

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

Installation

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


if (!require("BiocManager", quietly = TRUE))
 install.packages("BiocManager")
BiocManager::install("zellkonverter")

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

Documentation

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

browseVignettes("zellkonverter")

Converting to/from AnnData to SingleCellExperiments HTML R Script

Reference Manual PDF

NEWS Text

LICENSE Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews DataImport, DataRepresentation, SingleCell, Software

Version 1.16.0

In Bioconductor since BioC 3.12 (R-4.0) (4.5 years)

License MIT + file LICENSE

Depends

Imports basilisk, cli, DelayedArray, Matrix, methods, reticulate, S4Vectors, SingleCellExperiment(>= 1.11.6), SummarizedExperiment, utils

System Requirements

URL https://github.com/theislab/zellkonverter

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

Suggests anndata, BiocFileCache, BiocStyle, covr, HDF5Array, knitr, pkgload, rhdf5(>= 2.45.1), rmarkdown, scRNAseq, spelling, testthat, withr

Linking To

Enhances

Depends On Me scATAC.Explorer, OSCA.intro

Imports Me BgeeDB, singleCellTK, velociraptor

Suggests Me cellxgenedp, CuratedAtlasQueryR, GloScope, HDF5Array, HCATonsilData

Links To Me

Build Report Build Report

Package Archives

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

Source Package zellkonverter_1.16.0.tar.gz

Windows Binary (x86_64) zellkonverter_1.16.0.zip

macOS Binary (x86_64) zellkonverter_1.16.0.tgz

macOS Binary (arm64) zellkonverter_1.16.0.tgz

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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