Single-cell analysis toolkit for gene expression data in R


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Documentation for package ‘scater’ version 1.6.3

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A B C D E F G I K M N P R S T U

scater-package Single-cell analysis toolkit for expression in R

-- A --

accessors Additional accessors for the typical elements of a SingleCellExperiment object.
areSizeFactorsCentred Check if the size factors are centred at unity
arrange Arrange columns (cells) of a SingleCellExperiment object
arrange-method Arrange columns (cells) of a SingleCellExperiment object

-- B --

bootstraps Accessor and replacement for bootstrap results in a 'SingleCellExperiment' object
bootstraps-method Accessor and replacement for bootstrap results in a 'SingleCellExperiment' object
bootstraps<- Accessor and replacement for bootstrap results in a 'SingleCellExperiment' object
bootstraps<--method Accessor and replacement for bootstrap results in a 'SingleCellExperiment' object

-- C --

calcAverage Calculate average counts, adjusting for size factors or library size
calcIsExprs Calculate which features are expressed in which cells using a threshold on observed counts, transcripts-per-million, counts-per-million, FPKM, or defined expression levels.
calculateCPM Calculate counts per million (CPM)
calculateFPKM Calculate fragments per kilobase of exon per million reads mapped (FPKM)
calculateQCMetrics Calculate QC metrics
calculateTPM Calculate transcripts-per-million (TPM)

-- D --

deprecated Retrieve a representation of gene expression
downsampleCounts Downsample a count matrix

-- E --

exprs Additional accessors for the typical elements of a SingleCellExperiment object.
exprs,SingleCellExperiment-method, Additional accessors for the typical elements of a SingleCellExperiment object.
exprs<--method Additional accessors for the typical elements of a SingleCellExperiment object.

-- F --

filter Return 'SingleCellExperiment' with cells matching conditions.
filter-method Return 'SingleCellExperiment' with cells matching conditions.
findImportantPCs Find most important principal components for a given variable
fpkm Additional accessors for the typical elements of a SingleCellExperiment object.
fpkm<- Additional accessors for the typical elements of a SingleCellExperiment object.
fromCellDataSet Retrieve a representation of gene expression

-- G --

getBMFeatureAnnos Get feature annotation information from Biomart
getExprs Retrieve a representation of gene expression

-- I --

isOutlier Identify if a cell is an outlier based on a metric

-- K --

kallisto-wrapper kallisto wrapper functions

-- M --

multiplot Multiple plot function for ggplot2 plots
mutate Add new variables to 'colData(object)'.
mutate-method Add new variables to 'colData(object)'.

-- N --

newSCESet Create a new SCESet object
nexprs Count the number of expressed genes per cell
normalise Normalise a SingleCellExperiment object using pre-computed size factors
normalise-method Normalise a SingleCellExperiment object using pre-computed size factors
normaliseExprs Normalise expression expression levels for an SingleCellExperiment object
normalize Normalise a SingleCellExperiment object using pre-computed size factors
normalize-method Normalise a SingleCellExperiment object using pre-computed size factors
normalizeExprs Normalise expression expression levels for an SingleCellExperiment object
normalizeSCE Normalise a SingleCellExperiment object using pre-computed size factors
normliseExprs Normalise expression expression levels for an SingleCellExperiment object
norm_exprs Additional accessors for the typical elements of a SingleCellExperiment object.
norm_exprs<- Additional accessors for the typical elements of a SingleCellExperiment object.

-- P --

plotCellData Plot cell phenotype data from an SingleCellExperiment object
plotColData Plot cell phenotype data from an SingleCellExperiment object
plotDiffusionMap Plot a diffusion map for a SingleCellExperiment object
plotDiffusionMap-method Plot a diffusion map for a SingleCellExperiment object
plotExplanatoryVariables Plot explanatory variables ordered by percentage of phenotypic variance explained
plotExpression Plot expression values for a set of features (e.g. genes or transcripts)
plotExpression-method Plot expression values for a set of features (e.g. genes or transcripts)
plotExpressionDefault Plot expression values for a set of features (e.g. genes or transcripts)
plotExprsFreqVsMean Plot frequency of expression against mean expression level
plotExprsVsTxLength Plot expression against transcript length
plotFeatureData Plot feature (gene) data from a SingleCellExperiment object
plotHighestExprs Plot the features with the highest expression values
plotMDS Produce a multidimensional scaling plot for a SingleCellExperiment object
plotMDS-method Produce a multidimensional scaling plot for a SingleCellExperiment object
plotMetadata Plot metadata for cells or features
plotPCA Plot PCA for a SingleCellExperiment object
plotPCA-method Plot PCA for a SingleCellExperiment object
plotPCASCE Plot PCA for a SingleCellExperiment object
plotPhenoData Plot cell phenotype data from an SingleCellExperiment object
plotPlatePosition Plot cells in plate positions
plotQC Produce QC diagnostic plots
plotReducedDim Plot reduced dimension representation of cells
plotReducedDim-method Plot reduced dimension representation of cells
plotReducedDimDefault Plot reduced dimension representation of cells
plotRLE Plot a relative log expression (RLE) plot
plotRLE-method Plot a relative log expression (RLE) plot
plotRowData Plot feature (gene) data from a SingleCellExperiment object
plotScater Plot an overview of expression for each cell
plotTSNE Plot t-SNE for an SingleCellExperiment object
plotTSNE-method Plot t-SNE for an SingleCellExperiment object

-- R --

read10XResults Load in data from 10x experiment
read10xResults Load in data from 10x experiment
readKallistoResults kallisto wrapper functions
readKallistoResultsOneSample kallisto wrapper functions
readSalmonResults Salmon wrapper functions
readSalmonResultsOneSample Salmon wrapper functions
readTxResults Read transcript quantification data with tximport package
rename Rename variables of 'colData(object)'.
rename-method Rename variables of 'colData(object)'.
runDiffusionMap Plot a diffusion map for a SingleCellExperiment object
runKallisto kallisto wrapper functions
runPCA Plot PCA for a SingleCellExperiment object
runSalmon Salmon wrapper functions
runTSNE Plot t-SNE for an SingleCellExperiment object

-- S --

salmon-wrapper Salmon wrapper functions
scater_gui scater GUI function
SCESet The "Single Cell Expression Set" (SCESet) class
SCESet-class The "Single Cell Expression Set" (SCESet) class
sc_example_cell_info Cell information for the small example single-cell counts dataset to demonstrate capabilities of scater
sc_example_counts A small example of single-cell counts dataset to demonstrate capabilities of scater
stand_exprs Additional accessors for the typical elements of a SingleCellExperiment object.
stand_exprs<- Additional accessors for the typical elements of a SingleCellExperiment object.
summariseExprsAcrossFeatures Summarise expression values across feature

-- T --

toCellDataSet Retrieve a representation of gene expression
toSingleCellExperiment Convert an SCESet object to a SingleCellExperiment object

-- U --

updateSCESet Convert an SCESet object to a SingleCellExperiment object