zellkonverter

This is the development version of zellkonverter; for the stable release version, see zellkonverter.

Conversion Between scRNA-seq Objects

Bioconductor version: Development (3.22)

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: ORCID: 0000-0001-7744-8565 , github: lazappi), Aaron Lun [aut] (ORCID: ORCID: 0000-0002-3564-4813 , github: LTLA), Jack Kamm [ctb] (ORCID: ORCID: 0000-0003-2412-756X , github: jackkamm), 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")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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	1.19.3
In Bioconductor since	BioC 3.12 (R-4.0) (5 years)
License	MIT + file LICENSE
Depends
Imports	basilisk, cli, DelayedArray, Matrix, methods, reticulate, S4Vectors, SingleCellExperiment(>= 1.11.6), SparseArray, 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, SpatialExperiment, spelling, testthat, withr
Linking To
Enhances
Depends On Me	scATAC.Explorer, OSCA.intro
Imports Me	BgeeDB, DOtools, singleCellTK, velociraptor, OSTA
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_1.19.3.tar.gz
Windows Binary (x86_64)
macOS Binary (x86_64)	zellkonverter_1.19.2.tgz
macOS Binary (arm64)	zellkonverter_1.19.2.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/
Package Downloads Report	Download Stats