scater-package | Single-cell analysis toolkit for expression in R |
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 |
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 |
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) |
centreSizeFactors | Centre size factors at unity |
downsampleCounts | Downsample a count matrix |
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. |
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. |
getBMFeatureAnnos | Get feature annotation information from Biomart |
isOutlier | Identify outlier values |
kallisto-wrapper | kallisto wrapper functions |
librarySizeFactors | Compute library size factors |
multiplot | Multiple plot function for ggplot2 plots |
mutate | Add new variables to 'colData(object)'. |
mutate-method | Add new variables to 'colData(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 levels for a 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 levels for a SingleCellExperiment object |
normalizeSCE | Normalise a SingleCellExperiment object using pre-computed size factors |
normliseExprs | Normalise expression levels for a 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. |
plotCellData | Plot column metadata |
plotColData | Plot column metadata |
plotDiffusionMap | Plot specific reduced dimensions |
plotExplanatoryVariables | Plot explanatory variables ordered by percentage of phenotypic variance explained |
plotExpression | Plot expression values for all cells |
plotExprsFreqVsMean | Plot frequency against mean for each feature |
plotExprsVsTxLength | Plot expression against transcript length |
plotFeatureData | Plot row metadata |
plotHeatmap | Plot heatmap of gene expression values |
plotHighestExprs | Plot the highest expressing features |
plotMDS | Plot specific reduced dimensions |
plotPCA | Plot specific reduced dimensions |
plotPCA-method | Plot specific reduced dimensions |
plotPCASCE | Plot specific reduced dimensions |
plotPhenoData | Plot column metadata |
plotPlatePosition | Plot cells in plate positions |
plotQC | Produce QC diagnostic plots |
plotReducedDim | Plot reduced dimensions |
plotRLE | Plot a relative log expression (RLE) plot |
plotRLE-method | Plot a relative log expression (RLE) plot |
plotRowData | Plot row metadata |
plotScater | Plot an overview of expression for each cell |
plotTSNE | Plot specific reduced dimensions |
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 |
Reduced dimension plots | Plot specific reduced dimensions |
rename | Rename variables of 'colData(object)'. |
rename-method | Rename variables of 'colData(object)'. |
runDiffusionMap | Create a diffusion map from cell-level data |
runKallisto | kallisto wrapper functions |
runMDS | Perform MDS on cell-level data |
runPCA | Perform PCA on cell-level data |
runSalmon | Salmon wrapper functions |
runTSNE | Perform t-SNE on cell-level data |
salmon-wrapper | Salmon wrapper functions |
scater-plot-args | General visualization parameters |
scater-vis-var | Variable selection for visualization |
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 |
toSingleCellExperiment | Convert an SCESet object to a SingleCellExperiment object |
uniquifyFeatureNames | Make feature names unique |
updateSCESet | Convert an SCESet object to a SingleCellExperiment object |