scater: Single-cell analysis toolkit for gene expression data in R
Version 1.4.0

A collection of tools for doing various analyses of single-cell RNA-seq gene expression data, with a focus on quality control.

AuthorDavis McCarthy
Bioconductor views DataImport DataRepresentation DimensionReduction GeneExpression Infrastructure Normalization Preprocessing QualityControl RNASeq Sequencing SingleCell Software Transcriptomics Visualization
Date of publicationNone
MaintainerDavis McCarthy <davis@ebi.ac.uk>
LicenseGPL (>= 2)
Version1.4.0
URL http://bioconductor.org/packages/scater/
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("scater")

Getting started

Package overview
README.md
Introduction to `scater`: Single-cell analysis toolkit for expression in R

Popular man pages

calculateTPM: Calculate transcripts-per-million (TPM)
newSCESet: Create a new SCESet object.
plotRLE: Plot a relative log expression (RLE) plot
plotTSNE: Plot t-SNE for an SCESet object
read10XResults: Load in data from 10X experiment
readTxResults: Read transcript quantification data with tximport package
SCESet: The "Single Cell Expression Set" (SCESet) class
See all...

All man pages Function index File listing

Man pages

areSizeFactorsCentred: Check if the size factors are centred at unity
arrange: Arrange rows of 'pData(object)' by variables.
bootstraps: Accessor and replacement for bootstrap results in an SCESet...
calcAverage: Calculate average counts, adjusting for size factors or...
calcIsExprs: Calculate which features are expressed in which cells using a...
calculateCPM: Calculate counts per million (CPM)
calculateFPKM: Calculate fragments per kilobase of exon per million reads...
calculateQCMetrics: Calculate QC metrics
calculateTPM: Calculate transcripts-per-million (TPM)
cellNames: Get or set cell names from an SCESet object
cellPairwiseDistances: cellPairwiseDistances in an SCESet object
counts: Accessors for the 'counts' element of an SCESet object.
cpm: Accessors for the 'cpm' (counts per million) element of an...
fData: Replaces featureData in an SCESet object
featureControlInfo: featureControlInfo in an SCESet object
featurePairwiseDistances: featurePairwiseDistances in an SCESet object
filter: Return 'SCESet' with cells matching conditions.
findImportantPCs: Find most important principal components for a given variable
fpkm: Accessors for the 'fpkm' (fragments per kilobase of exon per...
fromCellDataSet: Convert a 'CellDataSet' to an 'SCESet'
getBMFeatureAnnos: Get feature annotation information from Biomart
get_exprs: Generic accessor for expression data from an SCESet object.
getExprs: Retrieve a representation of gene expression
is_exprs: Accessors for the 'is_exprs' element of an SCESet object.
isOutlier: Identify if a cell is an outlier based on a metric
isSpike: Get spike-in features in an SCESet object
mergeSCESet: Merge SCESet objects
multiplot: Multiple plot function for ggplot2 plots
mutate: Add new variables to 'pData(object)'.
newSCESet: Create a new SCESet object.
nexprs: Count the number of expressed genes per cell
normaliseExprs: Normalise expression expression levels for an SCESet object
normalize: Normalise an SCESet object using pre-computed size factors
norm_counts: Accessors for the 'norm_counts' element of an SCESet object.
norm_cpm: Accessors for the 'norm_cpm' (normalised counts per million)...
norm_exprs: Accessors for the 'norm_exprs' (normalised expression)...
norm_fpkm: Accessors for the 'norm_fpkm' (normalised fragments per...
norm_tpm: Accessors for the 'norm_tpm' (transcripts per million)...
pData: Replaces phenoData in an SCESet object
plot: Plot an overview of expression for each cell
plotDiffusionMap: Plot a diffusion map for an SCESet object
plotExplanatoryVariables: Plot explanatory variables ordered by percentage of...
plotExpression: Plot expression values for a set of features (e.g. genes or...
plotExprsFreqVsMean: Plot frequency of expression against mean expression level
plotExprsVsTxLength: Plot expression against transcript length
plotFeatureData: Plot feature (gene) data from an SCESet object
plotHighestExprs: Plot the features with the highest expression values
plotMDS: Produce a multidimensional scaling plot for an SCESet object
plotMetadata: Plot metadata for cells or features
plotPCA: Plot PCA for an SCESet object
plotPhenoData: Plot phenotype data from an SCESet object
plotPlatePosition: Plot cells in plate positions
plotQC: Produce QC diagnostic plots
plotReducedDim: Plot reduced dimension representation of cells
plotRLE: Plot a relative log expression (RLE) plot
plotTSNE: Plot t-SNE for an SCESet object
read10XResults: Load in data from 10X experiment
readKallistoResults: Read kallisto results from a batch of jobs
readKallistoResultsOneSample: Read kallisto results for a single sample into a list
readSalmonResults: Read Salmon results from a batch of jobs
readSalmonResultsOneSample: Read Salmon results for a single sample into a list
readTxResults: Read transcript quantification data with tximport package
reducedDimension: Reduced dimension representation for cells in an SCESet...
rename: Rename variables of 'pData(object)'.
runKallisto: Run kallisto on FASTQ files to quantify feature abundance
runSalmon: Run Salmon on FASTQ files to quantify feature abundance
scater_gui: scater GUI function
scater-package: Single-cell analysis toolkit for expression in R
SCESet: The "Single Cell Expression Set" (SCESet) class
SCESet-subset: Subsetting SCESet Objects
sc_example_cell_info: Cell information for the small example single-cell counts...
sc_example_counts: A small example of single-cell counts dataset to demonstrate...
set_exprs: Assignment method for the new elements of an SCESet object.
setSpike: Set spike-in features in an SCESet object
sizeFactors: Accessors size factors of an SCESet object.
spikes: Extract expression values for spike-in features in an SCESet...
stand_exprs: Accessors for the 'stand_exprs' (standardised expression)...
summariseExprsAcrossFeatures: Summarise expression values across feature
toCellDataSet: Convert an 'SCESet' to a 'CellDataSet'
tpm: Accessors for the 'tpm' (transcripts per million) element of...
updateSCESet: Update an SCESet object to the current version
whichSpike: Identify spike-in feature control sets in an SCESet object
writeSCESet: Write an SCESet object to an HDF5 file

Functions

Files

DESCRIPTION
NAMESPACE
R
R/10ximport-wrapper.R
R/AllClasses.R
R/AllGenerics.R
R/SCESet-methods.R
R/calculate-expression.R
R/cxx_utils.R
R/feature-preprocessing.R
R/gui.R
R/kallisto-wrapper.R
R/magic.R
R/normalisation.R
R/plotting.R
R/qc.R
R/salmon-wrapper.R
R/sc_example_cell_info-data.R
R/sc_example_counts-data.R
R/scater-package.R
R/test.R
R/tximport-wrapper.R
R/utils.R
R/verbs.R
README.md
build
build/vignette.rds
data
data/sc_example_cell_info.RData
data/sc_example_counts.RData
inst
inst/CITATION
inst/NEWS.Rd
inst/doc
inst/doc/vignette.R
inst/doc/vignette.Rmd
inst/doc/vignette.html
inst/extdata
inst/extdata/reads_1.fastq.gz
inst/extdata/reads_2.fastq.gz
inst/extdata/targets.txt
inst/extdata/transcripts.idx
inst/scater_qc_workflow.png
inst/scater_sticker.svg
inst/scater_sticker_300dpi.pdf
inst/scater_sticker_300dpi.png
inst/scater_sticker_small.png
inst/scater_sticker_web.pdf
inst/server.R
inst/shiny-app.R
inst/sticker_readme.md
inst/ui.R
inst/www
inst/www/scater_qc_workflow.png
man
man/SCESet-subset.Rd
man/SCESet.Rd
man/areSizeFactorsCentred.Rd
man/arrange.Rd
man/bootstraps.Rd
man/calcAverage.Rd
man/calcIsExprs.Rd
man/calculateCPM.Rd
man/calculateFPKM.Rd
man/calculateQCMetrics.Rd
man/calculateTPM.Rd
man/cellNames.Rd
man/cellPairwiseDistances.Rd
man/counts.Rd
man/cpm.Rd
man/fData.Rd
man/featureControlInfo.Rd
man/featurePairwiseDistances.Rd
man/filter.Rd
man/findImportantPCs.Rd
man/fpkm.Rd
man/fromCellDataSet.Rd
man/getBMFeatureAnnos.Rd
man/getExprs.Rd
man/get_exprs.Rd
man/isOutlier.Rd
man/isSpike.Rd
man/is_exprs.Rd
man/mergeSCESet.Rd
man/multiplot.Rd
man/mutate.Rd
man/newSCESet.Rd
man/nexprs.Rd
man/norm_counts.Rd
man/norm_cpm.Rd
man/norm_exprs.Rd
man/norm_fpkm.Rd
man/norm_tpm.Rd
man/normaliseExprs.Rd
man/normalize.Rd
man/pData.Rd
man/plot.Rd
man/plotDiffusionMap.Rd
man/plotExplanatoryVariables.Rd
man/plotExpression.Rd
man/plotExprsFreqVsMean.Rd
man/plotExprsVsTxLength.Rd
man/plotFeatureData.Rd
man/plotHighestExprs.Rd
man/plotMDS.Rd
man/plotMetadata.Rd
man/plotPCA.Rd
man/plotPhenoData.Rd
man/plotPlatePosition.Rd
man/plotQC.Rd
man/plotRLE.Rd
man/plotReducedDim.Rd
man/plotTSNE.Rd
man/read10XResults.Rd
man/readKallistoResults.Rd
man/readKallistoResultsOneSample.Rd
man/readSalmonResults.Rd
man/readSalmonResultsOneSample.Rd
man/readTxResults.Rd
man/reducedDimension.Rd
man/rename.Rd
man/runKallisto.Rd
man/runSalmon.Rd
man/sc_example_cell_info.Rd
man/sc_example_counts.Rd
man/scater-package.Rd
man/scater_gui.Rd
man/setSpike.Rd
man/set_exprs.Rd
man/sizeFactors.Rd
man/spikes.Rd
man/stand_exprs.Rd
man/summariseExprsAcrossFeatures.Rd
man/toCellDataSet.Rd
man/tpm.Rd
man/updateSCESet.Rd
man/whichSpike.Rd
man/writeSCESet.Rd
src
src/calc_exprs.cpp
src/init.cpp
src/matrix_info.cpp
src/scater.h
src/utils.cpp
tests
tests/testthat
tests/testthat.R
tests/testthat/test-SCESet-methods.R
tests/testthat/test-calculate-expression.R
tests/testthat/test-classes.R
tests/testthat/test-feature-preprocessing.R
tests/testthat/test-kallisto-wrapper.R
tests/testthat/test-magic.R
tests/testthat/test-normalisation.R
tests/testthat/test-plotting.R
tests/testthat/test-qc.R
tests/testthat/test-summariseExprsAcrossFeatures.R
tests/testthat/test-tximport-wrapper.R
tests/testthat/test-verbs.R
vignettes
vignettes/vignette.Rmd
scater documentation built on May 20, 2017, 10:39 p.m.

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