scater: single-cell analysis toolkit for expression with R
This package contains tools for the analysis of single-cell gene expression data using the statistical software R. The package places an emphasis on tools for quality control, visualisation and pre-processing of data before further downstream analysis.
We hope that
scater fills a useful niche between raw RNA-sequencing
count or transcripts-per-million data and more focused downstream
scater enables the following:
- Automated computation of QC metrics
- Transcript quantification from read data with pseudo-alignment
- Rich visualisations for exploratory analysis
- Seamless integration into the Bioconductor universe using the
- Simple normalisation methods and tight integration with the
See below for information about installation, getting started and highlights of the package.
Installation from Bioconductor (recommended)
scater package has been accepted into Bioconductor!
Thus, the most reliable way to install the package is to use the usual
## try http:// if https:// URLs are not supported source("https://bioconductor.org/biocLite.R") biocLite("scater")
scater package has been available as a "release" version in
the Bioconductor since April 2016. The release version of
scater works with
the release version of R and Bioconductor, and development will continue in the
devel version of the package on Bioconductor. Future releases will follow the
regular Bioconductor release cycle.
Using the most recent version of R is strongly recommended (R 3.4 at the time of writing). Effort has been made to ensure the package works with R >3.0, but the package has not been tested with R <3.1.1.
There are several other packages from CRAN and Bioconductor that
installing through Bioconductor will install these packages as well.
The following optional packages are not strictly required but enhance the
install.packages(c("cowplot", "cluster", "mvoutlier", "parallel", "Rtsne")) biocLite(c("destiny", "monocle"))
You might also like to install
dplyr for convenient data manipulation:
The best place to start is the vignette. From inside an R session, load
and then browse the vignettes:
There is a detailed HTML document available that introduces the main features
and functionality of
The step-by-step workflow offers
further examples of using
scran for low-level analysis of
The diagram below provised an overview of the pre-processing and QC workflow possible in
scater, listing the functions that can be used at various stages. A first place to start is with the
newSCESet function, which will allow you to create a data object for use with
scater package allows you to do some neat things relatively quickly. Some highlights are shown below with example code and screenshots.
- Automated computation of QC metrics
- Transcript quantification from read data with pseudo-alignment approaches
- Data format standardisation
- Rich visualisations for QC and exploratory analysis
- Seamless integration into the Bioconductor universe
- Simple normalisation methods
For details of how to use these functions, please consult the vignette and package documentation. The plots shown use the example data included with the package (for which there is no interesting structure) and as shown require only one or two lines of code to generate.
Automatic computation of QC metrics
calculateQCMetrics function to compute many metrics useful for gene/transcript-level and cell-level QC. Metrics computed include number of genes expressed per cell, percentage of expression from control genes (e.g. ERCC spike-ins) and many more.
Transcript quantification with
runSalmon functions provides wrappers to the
kallisto and 'Salmon' software for quantifying transcript abundance from FASTQ files using a "pseudo-alignment"" or "lightweight alignment" approaches. These new approaches are extremely fast while retaining accuracy. With
readSalmonResults, transcript quantities can be read into a data object in
plotScater for an SCESet object gives cumulative expression for the
most-expressed features (genes or transcripts)
plotTSNE function produces a t-distributed stochastic neighbour embedding
plot for the cells.
plotPCA function produces a principal components analysis plot for the
plotDiffusionMap function produces a diffusion map plot for the cells.
plotExpression function plots the expression values for a selection of
plotQC function produces a variety of QC plots useful for diagnostics and
feature and cell filtering. It can be used to plot the most highly-expressed
genes (or features) in the data set or create density plots to assess the
relative importance of explanatory variables, as well as many other
visualisations useful for QC.
plotPhenoData function plots two phenotype metadata variables (such as QC
plotFeatureData to plot feature (gene) metadata variables, including QC metrics.
Plus many, many more possibilities. Please consult the vignette and documentation for details.
Acknowledgements and disclaimer
The package leans heavily on previously published work and packages, namely
SingleCellExperiment class from the SingleCellExperiment
package (new for Bioconductor 3.6+) provides a modern data
structure to support single-cell analyses.
scater has adopted this data
structure from Bioconductor 3.6; wide adoption across Bioconductor will
streamline analysis workflows using multiple packages.
scater sticker is licensed under Creative Commons Attribution
CC-BY. Feel free to
share and adapt, but don't forget to credit the author. Skateboard icon made by
Nikita Golubev from
Flaticon is licensed by Creative Commons BY 3.0.
We hope the
scater package makes your life easier when analysing single-cell
RNA_seq data. Please do try it and contact us with bug reports, feedback, feature
requests, questions and suggestions to improve the package.
Davis McCarthy, September 2017
(on behalf of
scater authors and contributors)