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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 (3.20)

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 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>

Citation (from within R, enter citation("simpleSingleCell")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


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


To view documentation for the version of this package installed in your system, start R and enter:

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
13. Further analysis strategies HTML R Script


biocViews ImmunoOncologyWorkflow, SingleCellWorkflow, Workflow
Version 1.29.0
License Artistic-2.0
Imports utils, methods, knitr, callr, rmarkdown, CodeDepends, BiocStyle
System Requirements
See More
Suggests readxl, R.utils, SingleCellExperiment, scater, scran, limma, BiocFileCache,
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Depends On Me
Imports Me
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Package Archives

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

Source Package simpleSingleCell_1.29.0.tar.gz
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Source Repository git clone
Source Repository (Developer Access) git clone
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