simpleSingleCell

This is the released version of simpleSingleCell; for the devel version, see simpleSingleCell.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7

A step-by-step workflow for low-level analysis of single-cell RNA-seq data with Bioconductor

Bioconductor version: Release (3.23)

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.

Author: Aaron Lun [aut, cre], Davis McCarthy [aut], John Marioni [aut]

Maintainer: Aaron Lun <infinite.monkeys.with.keyboards at gmail.com>

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.

Installation

To install this package, start R (version "4.6") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("simpleSingleCell")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

No vignettes available

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	ImmunoOncologyWorkflow, SingleCellWorkflow, Workflow
Version	1.36.0
In Bioconductor since	BioC 3.7 (R-3.5) (8.5 years)
License	Artistic-2.0
Depends
Imports	utils, methods, knitr, callr, rmarkdown, CodeDepends, BiocStyle
System Requirements
URL	https://www.bioconductor.org/help/workflows/simpleSingleCell/

Suggests	readxl, R.utils, SingleCellExperiment, scater, scran, limma, BiocFileCache, org.Mm.eg.db
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	simpleSingleCell_1.36.0.tar.gz
Windows Binary (x86_64)
macOS Binary (big-sur-x86_64)
macOS Binary (sonoma-arm64)
Source Repository	git clone https://git.bioconductor.org/packages/simpleSingleCell
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/simpleSingleCell
Package Short Url	https://bioconductor.org/packages/simpleSingleCell/
Package Downloads Report	Download Stats