Man pages for scater
Single-Cell Analysis Toolkit for Gene Expression Data in R
| accessors | Additional accessors for the typical elements of a... |
| annotateBMFeatures | Get feature annotation information from Biomart |
| batchCorrectedAverages | Compute batch-corrected group-level averages |
| bootstraps | Accessor and replacement for bootstrap results in a... |
| defunct | Defunct functions |
| getExplanatoryPCs | Per-PC variance explained by a variable |
| getVarianceExplained | Per-gene variance explained by a variable |
| ggsce | Create a ggplot from a SingleCellExperiment |
| multiplot | Multiple plot function for ggplot2 plots |
| nexprs | Count the number of non-zero counts per cell or feature |
| plotColData | Plot column metadata |
| 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... |
| plotExpression | Plot expression values for all cells |
| plotGroupedHeatmap | Plot heatmap of group-level expression averages |
| plotHeatmap | Plot heatmap of gene expression values |
| plotHighestExprs | Plot the highest expressing features |
| plotPlatePosition | Plot cells in plate positions |
| plot_reddim | Plot specific reduced dimensions |
| plotReducedDim | Plot reduced dimensions |
| plotRLE | Plot relative log expression |
| plotRowData | Plot row metadata |
| plotScater | Plot an overview of expression for each cell |
| reexports | Objects exported from other packages |
| 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 |
| runTSNE | Perform t-SNE on cell-level data |
| runUMAP | Perform UMAP on cell-level data |
| scater-pkg | The 'scater' package |
| scater-plot-args | General visualization parameters |
| SCESet | The "Single Cell Expression Set" (SCESet) class |
| toSingleCellExperiment | Convert an SCESet object to a SingleCellExperiment object |
