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 (3.9)

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, cell cycle phase identification, doublet detection and batch correction. Procedures to detect highly variable genes, significantly correlated genes and subpopulation-specific marker genes are also shown. These analyses are demonstrated on publicly available scRNA-seq data sets from a variety of protocols including SMART-seq2 and 10X Genomics.

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 "3.6") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
BiocManager::install("simpleSingleCell", version = "3.9")

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


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HTML R Script 01. Introduction
HTML R Script 02. Read count data
HTML R Script 03. UMI count data
HTML R Script 04. Droplet-based data
HTML R Script 05. Correcting batch effects
HTML R Script 06. Quality control details
HTML R Script 07. Spike-in normalization
HTML R Script 08. Detecting doublets
HTML R Script 09. Advanced variance modelling
HTML R Script 10. Detecting differential expression
HTML R Script 11. Scalability for big data
HTML R Script 12. Further analysis strategies


biocViews ImmunoOncologyWorkflow, SingleCellWorkflow, Workflow
Version 1.7.20
License Artistic-2.0
Imports BiocStyle, callr, rmarkdown
Suggests knitr, readxl, R.utils, Matrix, SingleCellExperiment, scater, scran, DropletUtils,,, TxDb.Mmusculus.UCSC.mm10.ensGene, dynamicTreeCut, cluster, igraph, Rtsne, pheatmap, limma, edgeR, BiocParallel, BiocFileCache, BiocNeighbors, BiocSingular, scRNAseq, TENxBrainData
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Source Package simpleSingleCell_1.7.20.tar.gz
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