DOI: 10.18129/B9.bioc.simpleSingleCell    

This package is for version 3.12 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: 3.12

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")):


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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


biocViews ImmunoOncologyWorkflow, SingleCellWorkflow, Workflow
Version 1.14.0
License Artistic-2.0
Imports utils, methods, knitr, callr, rmarkdown, CodeDepends, BiocStyle
Suggests readxl, R.utils, SingleCellExperiment, scater, scran, limma, BiocFileCache,
Depends On Me
Imports Me
Suggests Me
Links To Me

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Source Package simpleSingleCell_1.14.0.tar.gz
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