A B C D E F G I L M N P Q R S T U misc
addPerCellQC | Add QC to an SE |
addPerFeatureQC | Add QC to an SE |
aggregateAcrossCells | Aggregate expression values across groups of cells |
aggregateAcrossCells-method | Aggregate expression values across groups of cells |
aggregateAcrossFeatures | Sum counts across feature sets |
annotateBMFeatures | Get feature annotation information from Biomart |
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 |
calculateAverage | Calculate per-feature average counts |
calculateAverage-method | Calculate per-feature average counts |
calculateCPM | Calculate counts per million (CPM) |
calculateCPM-method | Calculate counts per million (CPM) |
calculateDiffusionMap | Create a diffusion map from cell-level data |
calculateDiffusionMap-method | Create a diffusion map from cell-level data |
calculateFPKM | Calculate FPKMs |
calculateMDS | Perform MDS on cell-level data |
calculateMDS-method | Perform MDS on cell-level data |
calculateNMF | Perform NMF on cell-level data |
calculateNMF-method | Perform NMF on cell-level data |
calculatePCA | Perform PCA on expression data |
calculatePCA-method | Perform PCA on expression data |
calculateQCMetrics | Defunct functions |
calculateTPM | Calculate TPMs |
calculateTPM-method | Calculate TPMs |
calculateTSNE | Perform t-SNE on cell-level data |
calculateTSNE-method | Perform t-SNE on cell-level data |
calculateUMAP | Perform UMAP on cell-level data |
calculateUMAP-method | Perform UMAP on cell-level data |
centreSizeFactors | Defunct functions |
computeLibraryFactors | Compute library size factors |
computeMedianFactors | Compute median-based size factors |
defunct | Defunct functions |
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. |
fpkm | Additional accessors for the typical elements of a SingleCellExperiment object. |
fpkm-method | Additional accessors for the typical elements of a SingleCellExperiment object. |
fpkm<- | Additional accessors for the typical elements of a SingleCellExperiment object. |
fpkm<--method | Additional accessors for the typical elements of a SingleCellExperiment object. |
getBMFeatureAnnos | Get feature annotation information from Biomart |
getExplanatoryPCs | Per-PC variance explained by a variable |
getVarianceExplained | Per-gene variance explained by a variable |
getVarianceExplained-method | Per-gene variance explained by a variable |
ggcells | Create a ggplot from a SingleCellExperiment |
ggfeatures | Create a ggplot from a SingleCellExperiment |
isOutlier | Identify outlier values |
librarySizeFactors | Compute library size factors |
librarySizeFactors-method | Compute library size factors |
logNormCounts | Compute log-normalized expression values |
logNormCounts-method | Compute log-normalized expression values |
makePerCellDF | Create a per-cell data.frame from a SingleCellDataFrame |
makePerFeatureDF | Create a per-feature data.frame from a SingleCellDataFrame |
medianSizeFactors | Compute median-based size factors |
medianSizeFactors-method | Compute median-based size factors |
mockSCE | Mock up a SingleCellExperiment |
multiplot | Multiple plot function for ggplot2 plots |
nexprs | Count the number of non-zero counts per cell or feature |
nexprs-method | Count the number of non-zero counts per cell or feature |
normalize-method | Defunct functions |
normalizeCounts | Compute normalized expression values |
normalizeCounts-method | Compute normalized expression values |
norm_exprs | Additional accessors for the typical elements of a SingleCellExperiment object. |
norm_exprs-method | Additional accessors for the typical elements of a SingleCellExperiment object. |
norm_exprs<- | Additional accessors for the typical elements of a SingleCellExperiment object. |
norm_exprs<--method | Additional accessors for the typical elements of a SingleCellExperiment object. |
numDetectedAcrossCells | Number of detected expression values per group of cells |
numDetectedAcrossCells-method | Number of detected expression values per group of cells |
numDetectedAcrossFeatures | Number of detected expression values per group of features |
numDetectedAcrossFeatures-method | Number of detected expression values per group of features |
perCellQCMetrics | Compute per-cell quality control metrics for a count matrix or a SingleCellExperiment. |
perCellQCMetrics-method | Compute per-cell quality control metrics for a count matrix or a SingleCellExperiment. |
perFeatureQCMetrics | Per-feature quality control metrics |
perFeatureQCMetrics-method | Per-feature quality control metrics |
plotColData | Plot column metadata |
plotDiffusionMap | Plot specific reduced dimensions |
plotDots | Create a dot plot of expression values |
plotExplanatoryPCs | Plot the explanatory PCs for each variable |
plotExplanatoryVariables | Plot explanatory variables ordered by percentage of variance explained |
plotExpression | Plot expression values for all cells |
plotHeatmap | Plot heatmap of gene expression values |
plotHighestExprs | Plot the highest expressing features |
plotMDS | Plot specific reduced dimensions |
plotNMF | Plot specific reduced dimensions |
plotPCA | Plot specific reduced dimensions |
plotPCA-method | Plot specific reduced dimensions |
plotPCASCE | Plot specific reduced dimensions |
plotPlatePosition | Plot cells in plate positions |
plotReducedDim | Plot reduced dimensions |
plotRLE | Plot relative log expression |
plotRLE-method | Plot relative log expression |
plotRowData | Plot row metadata |
plotScater | Plot an overview of expression for each cell |
plotTSNE | Plot specific reduced dimensions |
plotUMAP | Plot specific reduced dimensions |
quickPerCellQC | Quick cell-level QC |
readSparseCounts | Read sparse count matrix from file |
Reduced dimension plots | Plot specific reduced dimensions |
retrieveCellInfo | Cell-based data retrieval |
retrieveFeatureInfo | Feature-based data retrieval |
runColDataPCA | Perform PCA on column metadata |
runDiffusionMap | Create a diffusion map from cell-level data |
runMDS | Perform MDS on cell-level data |
runMultiUMAP | Multi-modal UMAP |
runNMF | Perform NMF on cell-level data |
runPCA | Perform PCA on expression data |
runPCA-method | Perform PCA on expression data |
runTSNE | Perform t-SNE on cell-level data |
runUMAP | Perform UMAP on cell-level data |
scater-plot-args | General visualization parameters |
scater-utils | Developer utilities |
SCESet | The "Single Cell Expression Set" (SCESet) class |
SCESet-class | The "Single Cell Expression Set" (SCESet) class |
sc_example_cell_info | Mock up a SingleCellExperiment |
sc_example_counts | Mock up a SingleCellExperiment |
stand_exprs | Additional accessors for the typical elements of a SingleCellExperiment object. |
stand_exprs,SingleCellExperiment-method, | Additional accessors for the typical elements of a SingleCellExperiment object. |
stand_exprs<- | Additional accessors for the typical elements of a SingleCellExperiment object. |
stand_exprs<--method | Additional accessors for the typical elements of a SingleCellExperiment object. |
sumCountsAcrossCells | Aggregate expression values across groups of cells |
sumCountsAcrossCells-method | Aggregate expression values across groups of cells |
sumCountsAcrossFeatures | Sum counts across feature sets |
sumCountsAcrossFeatures-method | Sum counts across feature sets |
toSingleCellExperiment | Convert an SCESet object to a SingleCellExperiment object |
uniquifyFeatureNames | Make feature names unique |
updateSCESet | Convert an SCESet object to a SingleCellExperiment object |
.assignIndicesToWorkers | Developer utilities |
.bpNotSharedOrUp | Developer utilities |
.splitColsByWorkers | Developer utilities |
.splitRowsByWorkers | Developer utilities |
.splitVectorByWorkers | Developer utilities |
.subset2index | Developer utilities |