zellkonverter
Conversion Between scRNA-seq Objects
Bioconductor version: Release (3.20)
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]
Maintainer: Luke Zappia <luke at lazappi.id.au>
, Aaron Lun [aut] , Jack Kamm [ctb] , Robrecht Cannoodt [ctb] (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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | DataImport, DataRepresentation, SingleCell, Software |
| Version | 1.16.0 |
| In Bioconductor since | BioC 3.12 (R-4.0) (4 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, 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.
| Source Package | zellkonverter_1.16.0.tar.gz |
| Windows Binary (x86_64) | zellkonverter_1.16.0.zip (64-bit only) |
| macOS Binary (x86_64) | zellkonverter_1.16.0.tgz |
| macOS Binary (arm64) | zellkonverter_1.16.0.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 |