Single-Cell Analysis Toolkit for Gene Expression Data in R

accessors | Additional accessors for the typical elements of a... |

arrange | Arrange columns (cells) of a SingleCellExperiment object |

bootstraps | Accessor and replacement for bootstrap results in a... |

calculateAverage | Calculate average counts, adjusting for size factors or... |

calculateCPM | Calculate counts per million (CPM) |

calculateFPKM | Calculate fragments per kilobase of exon per million reads... |

calculateQCMetrics | Calculate QC metrics |

calculateTPM | Calculate transcripts-per-million (TPM) |

centreSizeFactors | Centre size factors at unity |

filter | Return 'SingleCellExperiment' with cells matching conditions. |

getBMFeatureAnnos | Get feature annotation information from Biomart |

getExplanatoryPCs | Estimate the percentage of variance explained for each gene. |

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)'. |

nexprs | Count the number of non-zero counts per cell or feature |

normalize | Normalize a SingleCellExperiment object using pre-computed... |

normalizeCounts | Divide columns of a count matrix by the size factors |

plotColData | Plot column metadata |

plotExplanatoryPCs | Plot the explanatory PCs for each variable |

plotExplanatoryVariables | Plot explanatory variables ordered by percentage of variance... |

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 |

plotPlatePosition | Plot cells in plate positions |

plot_reddim | Plot specific reduced dimensions |

plotReducedDim | Plot reduced dimensions |

plotRLE | Plot a relative log expression (RLE) plot |

plotRowData | Plot row metadata |

plotScater | Plot an overview of expression for each cell |

readSparseCounts | Read sparse count matrix from file |

rename | Rename variables of 'colData(object)'. |

runDiffusionMap | Create a diffusion map from cell-level data |

runMDS | Perform MDS on cell-level data |

runPCA | Perform PCA on cell-level data |

runTSNE | Perform t-SNE on cell-level data |

runUMAP | Perform UMAP on cell-level data |

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

scater-plot-args | General visualization parameters |

scater-vis-var | Variable selection for visualization |

SCESet | The "Single Cell Expression Set" (SCESet) class |

sc_example_cell_info | Cell information for the small example single-cell counts... |

sc_example_counts | A small example of single-cell counts dataset to demonstrate... |

sumCountsAcrossFeatures | Sum counts across a feature set |

toSingleCellExperiment | Convert an SCESet object to a SingleCellExperiment object |

uniquifyFeatureNames | Make feature names unique |

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