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| scater-package | Single-cell analysis toolkit for expression in R |
| arrange | Arrange columns (cells) of a SingleCellExperiment object (deprecated). |
| arrange-method | Arrange columns (cells) of a SingleCellExperiment object (deprecated). |
| 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 |
| calculateAverage | Calculate average counts, adjusting for size factors or library size |
| 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 |
| 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 (deprecated). |
| filter-method | Return 'SingleCellExperiment' with cells matching conditions (deprecated). |
| 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 |
| getExplanatoryPCs | Estimate the percentage of variance explained for each PC. |
| getVarianceExplained | Estimate the percentage of variance explained for each gene. |
| isOutlier | Identify outlier values |
| librarySizeFactors | Compute library size factors |
| multiplot | Multiple plot function for ggplot2 plots |
| mutate | Add new variables to 'colData(object)' (deprecated). |
| mutate-method | Add new variables to 'colData(object)' (deprecated). |
| nexprs | Count the number of non-zero counts per cell or feature |
| normalize | Normalize a SingleCellExperiment object using pre-computed size factors |
| normalize-method | Normalize a SingleCellExperiment object using pre-computed size factors |
| normalizeCounts | Divide columns of a count matrix by the size factors |
| normalizeSCE | Normalize a SingleCellExperiment object using pre-computed size factors |
| norm_exprs | Additional accessors for the typical elements of a SingleCellExperiment object. |
| norm_exprs<- | Additional accessors for the typical elements of a SingleCellExperiment object. |
| plotColData | Plot column metadata |
| plotDiffusionMap | Plot specific reduced dimensions |
| 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 |
| plotExprsFreqVsMean | Plot frequency against mean for each feature |
| plotExprsVsTxLength | Plot expression against transcript length |
| 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 |
| plotPlatePosition | Plot cells in plate positions |
| 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 |
| plotUMAP | Plot specific reduced dimensions |
| readSparseCounts | Read sparse count matrix from file |
| Reduced dimension plots | Plot specific reduced dimensions |
| rename | Rename variables of 'colData(object)' (deprecated). |
| rename-method | Rename variables of 'colData(object)' (deprecated). |
| runDiffusionMap | Create a diffusion map from cell-level data |
| runMDS | Perform MDS on cell-level data |
| runPCA-method | Perform PCA on cell-level data |
| runTSNE | Perform t-SNE on cell-level data |
| runUMAP | Perform UMAP on cell-level data |
| scater-plot-args | General visualization parameters |
| scater-vis-var | Variable selection for visualization |
| 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. |
| sumCountsAcrossCells | Sum counts across a set of cells |
| sumCountsAcrossFeatures | Sum counts across a feature set |
| toSingleCellExperiment | Convert an SCESet object to a SingleCellExperiment object |
| uniquifyFeatureNames | Make feature names unique |
| updateSCESet | Convert an SCESet object to a SingleCellExperiment object |