zellkonverter

DOI: 10.18129/B9.bioc.zellkonverter  

Conversion Between scRNA-seq Objects

Bioconductor version: Release (3.18)

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	1.12.1
In Bioconductor since	BioC 3.12 (R-4.0) (3 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(>= 2.45.1), 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, CuratedAtlasQueryR, GloScope, HCATonsilData, HDF5Array
Links To Me
Build Report

Package Archives

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

Source Package	zellkonverter_1.12.1.tar.gz
Windows Binary	zellkonverter_1.12.1.zip
macOS Binary (x86_64)	zellkonverter_1.12.1.tgz
macOS Binary (arm64)
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 3.18	Source Archive