simpleSingleCell

DOI: 10.18129/B9.bioc.simpleSingleCell    

This is the development version of simpleSingleCell; for the stable release version, see simpleSingleCell.

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

Bioconductor version: Development (3.11)

Almost all content that was previously in these workflows have been migrated to the "Orchestrating Single-Cell Analyses with Bioconductor" book at https://osca.bioconductor.org. Most vignettes here are retained largely for back-compatibility with existing external links, and provide 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")):

Installation

To install this package, start R (version "4.0") and enter:

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 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
HTML R Script Redirection

Details

biocViews ImmunoOncologyWorkflow, SingleCellWorkflow, Workflow
Version 1.11.0
License Artistic-2.0
Depends
Imports
LinkingTo
Suggests knitr, rmarkdown, BiocStyle, 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_1.11.0.tar.gz
Windows Binary
Mac OS X 10.11 (El Capitan)
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

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