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Bioconductor - zellkonverter

zellkonverter

This is the released version of zellkonverter; for the devel version, see zellkonverter.

Conversion Between scRNA-seq Objects

Bioconductor version: Release (3.21)

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: 0000-0001-7744-8565 , Aaron Lun [aut] ORCID: 0000-0002-3564-4813 , Jack Kamm [ctb] ORCID: 0000-0003-2412-756X , Robrecht Cannoodt [ctb] (ORCID: ORCID: 0000-0003-3641-729X , github: rcannood), Gabriel Hoffman [ctb] (ORCID: ORCID: 0000-0002-0957-0224 , github: GabrielHoffman), Marek Cmero [ctb] (ORCID: ORCID: 0000-0001-7783-5530 , github: mcmero)

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

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

To install this package, start R (version "4.5") 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")

Details biocViews DataImport, DataRepresentation, SingleCell, Software Version 1.18.0 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 See More Suggests anndata, BiocFileCache, BiocStyle, covr, HDF5Array, knitr, pkgload, rhdf5(>= 2.45.1), rmarkdown, scRNAseq, SpatialExperiment, 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.

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