zellkonverter

DOI: 10.18129/B9.bioc.zellkonverter  

Conversion Between scRNA-seq Objects

Bioconductor version: Release (3.17)

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] , Aaron Lun [aut] , Jack Kamm [ctb] , Robrecht Cannoodt [ctb] (, rcannood)

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

Installation

To install this package, start R (version "4.3") 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")

 

HTML	R Script	Converting to/from AnnData to SingleCellExperiments
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	DataImport, DataRepresentation, SingleCell, Software
Version	1.10.1
In Bioconductor since	BioC 3.12 (R-4.0) (2.5 years)
License	MIT + file LICENSE
Depends
Imports	Matrix, basilisk, reticulate, SingleCellExperiment(>= 1.11.6), SummarizedExperiment, DelayedArray, methods, S4Vectors, utils, cli
LinkingTo
Suggests	anndata, BiocFileCache, BiocStyle, covr, HDF5Array, knitr, pkgload, rmarkdown, rhdf5, scRNAseq, spelling, testthat, withr
SystemRequirements
Enhances
URL	https://github.com/theislab/zellkonverter
BugReports	https://github.com/theislab/zellkonverter/issues
Depends On Me	OSCA.intro
Imports Me	singleCellTK, velociraptor
Suggests Me	cellxgenedp, HDF5Array
Links To Me
Build Report

Package Archives

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

Source Package	zellkonverter_1.10.1.tar.gz
Windows Binary	zellkonverter_1.10.1.zip
macOS Binary (x86_64)
macOS Binary (arm64)	zellkonverter_1.9.0.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/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.17	Source Archive