simpleSingleCell

DOI: 10.18129/B9.bioc.simpleSingleCell    

This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see simpleSingleCell.

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

Bioconductor version: 3.13

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>

Installation

To install this package, start R (version "4.1") and enter:

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

BiocManager::install("simpleSingleCell")

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("simpleSingleCell")

 

HTML		01. Introduction
HTML		02. Read count data
HTML		03. UMI count data
HTML		04. Droplet-based data
HTML		05. Correcting batch effects
HTML		06. Quality control details
HTML		07. Spike-in normalization
HTML		08. Detecting doublets
HTML		09. Advanced variance modelling
HTML		10. Detecting differential expression
HTML		11. Advanced batch correction
HTML		12. Scalability for big data
HTML	R Script	13. Further analysis strategies

Details

biocViews	ImmunoOncologyWorkflow, SingleCellWorkflow, Workflow
Version	1.16.0
License	Artistic-2.0
Depends
Imports	utils, methods, knitr, callr, rmarkdown, CodeDepends, BiocStyle
LinkingTo
Suggests	readxl, R.utils, SingleCellExperiment, scater, scran, limma, BiocFileCache, org.Mm.eg.db
SystemRequirements
Enhances
URL	https://www.bioconductor.org/help/workflows/simpleSingleCell/
Depends On Me
Imports Me
Suggests Me
Links To Me

Package Archives

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

Source Package	simpleSingleCell_1.16.0.tar.gz
Windows Binary
macOS 10.13 (High Sierra)
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