Workflow Package: simpleSingleCell

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

Bioconductor version: Release (3.7)

This workflow implements a low-level analysis pipeline for scRNA-seq data using scran, scater and other Bioconductor packages. It describes how to perform quality control on the libraries, normalization of cell-specific biases, basic data exploration and cell cycle phase identification. Procedures to detect highly variable genes, significantly correlated genes and subpopulation-specific marker genes are also shown. These analyses are demonstrated on a range of publicly available scRNA-seq data sets.

Author: Aaron Lun [aut, cre], Davis McCarthy [aut], John Marioni [aut]

Maintainer: Aaron Lun <alun at>


To install this package, start R and enter:

## try http:// if https:// URLs are not supported


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



HTML R Script Analyzing droplet-based scRNA-seq data
HTML R Script Analyzing scRNA-seq read count data
HTML R Script Analyzing scRNA-seq UMI count data
HTML R Script Correcting batch effects in scRNA-seq data
HTML R Script Further strategies for analyzing scRNA-seq data
HTML R Script Workflows for analyzing single-cell RNA-seq data with R/Bioconductor


biocViews SingleCellWorkflow, Workflow
Version 1.2.1
License Artistic-2.0
Depends R (>= 3.3.0), BiocStyle, knitr, BiocParallel, Rtsne, mvoutlier, destiny, readxl, gdata, SingleCellExperiment, scater,, scran, limma, pheatmap, dynamicTreeCut, cluster, edgeR, TxDb.Mmusculus.UCSC.mm10.ensGene, scRNAseq, DropletUtils
Suggests knitr, rmarkdown
Depends On Me
Imports Me
Suggests Me

Documentation »


R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: