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

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

AuthorDavis McCarthy
Date of publicationNone
MaintainerDavis McCarthy <davis@ebi.ac.uk>
LicenseGPL (>= 2)
Version1.2.0
https://github.com/davismcc/scater

View on Bioconductor

Man pages

arrange: Arrange rows of 'pData(object)' by variables.

bootstraps: Accessor and replacement for bootstrap results in an SCESet...

calcIsExprs: Calculate which features are expressed in which cells using a...

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

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

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

plotTSNE: Plot t-SNE for an SCESet object

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.

sizeFactors: Accessors size factors of an SCESet object.

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

writeSCESet: Write an SCESet object to an HDF5 file

Functions

arrange Man page
arrange.SCESet Man page
arrange,SCESet-method Man page
bootstraps Man page
bootstraps<- Man page
bootstraps.SCESet Man page
bootstraps<-,SCESet,array-method Man page
bootstraps,SCESet-method Man page
calcIsExprs Man page
calculateFPKM Man page
calculateQCMetrics Man page
calculateTPM Man page
cellDist Man page
cellDist<- Man page
cellDistSCESet Man page
cellDist<-,SCESet,dist-method Man page
cellDist<-,SCESet,matrix-method Man page
cellDist,SCESet-method Man page
cellNames Man page
cellNames<- Man page
cellNames<-,SCESet,vector-method Man page
cellPairwiseDistances Man page
cellPairwiseDistances<- Man page
cellPairwiseDistances.SCESet Man page
cellPairwiseDistances<-,SCESet,dist-method Man page
cellPairwiseDistances<-,SCESet,matrix-method Man page
cellPairwiseDistances,SCESet-method Man page
counts Man page
counts.SCESet Man page
counts<-,SCESet,matrix-method Man page
counts,SCESet-method Man page
cpm Man page
cpm<- Man page
cpmSCESet Man page
cpm<-,SCESet,matrix-method Man page
cpm,SCESet-method Man page
fData Man page
fData<-,SCESet,AnnotatedDataFrame-method Man page
fData<-,SCESet,data.frame-method Man page
fData,SCESet-method Man page
featDist Man page
featDist<- Man page
featDistSCESet Man page
featDist<-,SCESet,dist-method Man page
featDist<-,SCESet,matrix-method Man page
featDist,SCESet-method Man page
featurePairwiseDistances Man page
featurePairwiseDistances<- Man page
featurePairwiseDistancesSCESet Man page
featurePairwiseDistances<-,SCESet,dist-method Man page
featurePairwiseDistances<-,SCESet,matrix-method Man page
featurePairwiseDistances,SCESet-method Man page
filter Man page
filter.SCESet Man page
filter,SCESet-method Man page
findImportantPCs Man page
fpkm Man page
fpkm<- Man page
fpkm.SCESet Man page
fpkm<-,SCESet,matrix-method Man page
fpkm,SCESet-method Man page
fromCellDataSet Man page
getBMFeatureAnnos Man page
get_exprs Man page
getExprs Man page
get_exprs.SCESet Man page
get_exprs,SCESet-method Man page
is_exprs Man page
is_exprs<- Man page
is_exprs.SCESet Man page
is_exprs<-,SCESet,matrix-method Man page
is_exprs,SCESet-method Man page
isOutlier Man page
mergeSCESet Man page
multiplot Man page
mutate Man page
mutate.SCESet Man page
mutate,SCESet-method Man page
newSCESet Man page
nexprs Man page
normalise Man page
normaliseExprs Man page
normalise,SCESet-method Man page
normalize Man page
normalizeExprs Man page
normalize.SCESet Man page
normalize,SCESet-method Man page
norm_counts Man page
norm_counts<- Man page
norm_counts.SCESet Man page
norm_counts<-,SCESet,matrix-method Man page
norm_counts,SCESet-method Man page
norm_cpm Man page
norm_cpm<- Man page
norm_cpm.SCESet Man page
norm_cpm<-,SCESet,matrix-method Man page
norm_cpm,SCESet-method Man page
norm_exprs Man page
norm_exprs<- Man page
norm_exprs.SCESet Man page
norm_exprs<-,SCESet,matrix-method Man page
norm_exprs,SCESet-method Man page
norm_fpkm Man page
norm_fpkm<- Man page
norm_fpkm.SCESet Man page
norm_fpkm<-,SCESet,matrix-method Man page
norm_fpkm,SCESet-method Man page
normliseExprs Man page
norm_tpm Man page
norm_tpm<- Man page
norm_tpm.SCESet Man page
norm_tpm<-,SCESet,matrix-method Man page
norm_tpm,SCESet-method Man page
pData Man page
pData<-,SCESet,AnnotatedDataFrame-method Man page
pData<-,SCESet,data.frame-method Man page
pData,SCESet-method Man page
plot Man page
plotDiffusionMap Man page
plotDiffusionMapSCESet Man page
plotDiffusionMap,SCESet-method Man page
plotExplanatoryVariables Man page
plotExpression Man page
plotExpression,data.frame-method Man page
plotExpressionDefault Man page
plotExpressionSCESet Man page
plotExpression,SCESet-method Man page
plotExprsFreqVsMean Man page
plotExprsVsTxLength Man page
plotFeatureData Man page
plotHighestExprs Man page
plotMDS Man page
plotMDSSCESet Man page
plotMDS,SCESet-method Man page
plotMetadata Man page
plotPCA Man page
plotPCASCESet Man page
plotPCA,SCESet-method Man page
plotPhenoData Man page
plotPlatePosition Man page
plotQC Man page
plotReducedDim Man page
plotReducedDIm Man page
plotReducedDim,data.frame-method Man page
plotReducedDim.default Man page
plotReducedDim.SCESet Man page
plotReducedDim,SCESet-method Man page
plotSCESet Man page
plot,SCESet,ANY-method Man page
plot,SCESet-method Man page
plotTSNE Man page
plotTSNE,SCESet-method Man page
readKallistoResults Man page
readKallistoResultsOneSample Man page
readSalmonResults Man page
readSalmonResultsOneSample Man page
readTxResults Man page
redDim Man page
redDim<- Man page
redDim.SCESet Man page
redDim<-,SCESet,matrix-method Man page
redDim,SCESet-method Man page
reducedDimension Man page
reducedDimension<- Man page
reducedDimension.SCESet Man page
reducedDimension<-,SCESet,matrix-method Man page
reducedDimension,SCESet-method Man page
rename Man page
rename.SCESet Man page
rename,SCESet-method Man page
runKallisto Man page
runSalmon Man page
scater_gui Man page
scater-package Man page
SCESet Man page
[,SCESet,ANY,ANY,ANY-method Man page
[,SCESet,ANY,ANY-method Man page
[,SCESet,ANY-method Man page
SCESet-class Man page
[,SCESet-method Man page
SCESet-subset Man page
sc_example_cell_info Man page
sc_example_counts Man page
set_exprs Man page
set_exprs<- Man page
set_exprs<-,SCESet,ANY,matrix-method Man page
set_exprs<-,SCESet,ANY,NULL-method Man page
sizeFactors Man page
sizeFactors<- Man page
sizeFactors.SCESet Man page
sizeFactors,SCESet-method Man page
sizeFactors<-,SCESet,NULL-method Man page
sizeFactors<-,SCESet,numeric-method Man page
stand_exprs Man page
stand_exprs<- Man page
stand_exprs.SCESet Man page
stand_exprs<-,SCESet,matrix-method Man page
stand_exprs,SCESet-method Man page
summariseExprsAcrossFeatures Man page
toCellDataSet Man page
tpm Man page
tpm<- Man page
tpm.SCESet Man page
tpm<-,SCESet,matrix-method Man page
tpm,SCESet-method Man page
updateSCESet Man page
writeSCESet Man page

Files

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

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