zellkonverter
This is the released version of zellkonverter; for the devel version, see zellkonverter.
Conversion Between scRNA-seq Objects
Bioconductor version: Release (3.23)
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:
, github: lazappi), Aaron Lun [aut] (ORCID:
, github: LTLA), Jack Kamm [ctb] (ORCID:
, github: jackkamm), Robrecht Cannoodt [ctb] (ORCID:
, github: rcannood), Gabriel Hoffman [ctb] (ORCID:
, github: GabrielHoffman), Marek Cmero [ctb] (ORCID:
, github: mcmero)
Maintainer: Luke Zappia <luke at lazappi.id.au>
citation("zellkonverter")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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 | 1.22.0 |
| In Bioconductor since | BioC 3.12 (R-4.0) (6 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 |
See More
| 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 | BatChef, BgeeDB, DOtools, singleCellTK, velociraptor |
| Suggests Me | cellxgenedp, CuratedAtlasQueryR, GloScope, HDF5Array, HCATonsilData, nemoR |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | zellkonverter_1.22.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | zellkonverter_1.22.0.tgz |
| macOS Binary (sonoma-arm64) | zellkonverter_1.22.0.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 3.23 | Source Archive |