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zellkonverter

Conversion Between scRNA-seq Objects


Bioconductor version: Release (3.19)

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>

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

Details

biocViews DataImport, DataRepresentation, SingleCell, Software
Version 1.14.0
In Bioconductor since BioC 3.12 (R-4.0) (3.5 years)
License MIT + file LICENSE
Depends
Imports Matrix, basilisk, reticulate, SingleCellExperiment(>= 1.11.6), SummarizedExperiment, DelayedArray, methods, S4Vectors, utils, cli
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, rmarkdown, rhdf5(>= 2.45.1), scRNAseq, spelling, testthat, withr
Linking To
Enhances
Depends On Me OSCA.intro
Imports Me 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_1.14.0.tar.gz
Windows Binary zellkonverter_1.14.0.zip (64-bit only)
macOS Binary (x86_64) zellkonverter_1.14.0.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 3.19 Source Archive