simpleSingleCell
A step-by-step workflow for low-level analysis of single-cell RNA-seq data with Bioconductor
Bioconductor version: 3.23 · Package version: 1.36.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
Once a proud workflow package, this is now a shell of its former self. Almost all of its content has been cannibalized for use in the "Orchestrating Single-Cell Analyses with Bioconductor" book at https://osca.bioconductor.org. Most vignettes here are retained as reminders of the glory that once was, also providing redirection for existing external links to the relevant OSCA book chapters.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("simpleSingleCell")Details
| Maintainer | Aaron Lun <infinite.monkeys.with.keyboards@gmail.com> |
| Author | Aaron Lun [aut, cre], Davis McCarthy [aut], John Marioni [aut] |
| License | Artistic-2.0 |
| URL | https://www.bioconductor.org/help/workflows/simpleSingleCell/ |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | ImmunoOncologyWorkflow, SingleCellWorkflow, Workflow |
| Package Short Url | https://bioconductor.org/packages/simpleSingleCell/ |
Citation
From within R, enter citation("simpleSingleCell"):
Aaron Lun, Davis McCarthy, John Marioni. simpleSingleCell: A step-by-step workflow for low-level analysis of single-cell RNA-seq data with Bioconductor. doi:10.18129/B9.bioc.simpleSingleCell, R package version 1.36.0, https://bioconductor.org/packages/simpleSingleCell.
Generated from the package metadata; it may differ from the package's own citation.
Download
Follow the installation instructions to use this package in your R session.
| Source package | simpleSingleCell_1.36.0.tar.gz |
Dependencies
Imports: utils, methods, knitr, callr, rmarkdown, CodeDepends, BiocStyle
Suggests: readxl, R.utils, SingleCellExperiment, scater, scran, limma, BiocFileCache, org.Mm.eg.db