DOI: 10.18129/B9.bioc.simpleSingleCell    

This package is for version 3.11 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: 3.11

Almost all content that was previously in these workflows have been migrated to the "Orchestrating Single-Cell Analyses with Bioconductor" book at 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>

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


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HTML R Script 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 1.12.0
License Artistic-2.0
Suggests knitr, rmarkdown, BiocStyle, 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_1.12.0.tar.gz
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