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

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

Author
Davis McCarthy
Date of publication
None
Maintainer
Davis McCarthy <davis@ebi.ac.uk>
License
GPL (>= 2)
Version
1.2.0
URLs

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

Files in this package

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