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A B C D E F G I K M N P R S T U
| scater-package | Single-cell analysis toolkit for expression in R |
| accessors | Additional accessors for the typical elements of a SingleCellExperiment object. |
| 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) |
| deprecated | Retrieve a representation of gene expression |
| 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. |
| fromCellDataSet | Retrieve a representation of gene expression |
| getBMFeatureAnnos | Get feature annotation information from Biomart |
| getExprs | Retrieve a representation of gene expression |
| isOutlier | Identify if a cell is an outlier based on a metric |
| kallisto-wrapper | kallisto wrapper functions |
| multiplot | Multiple plot function for ggplot2 plots |
| mutate | Add new variables to 'colData(object)'. |
| mutate-method | Add new variables to 'colData(object)'. |
| newSCESet | Create a new SCESet 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 expression levels for an 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 expression levels for an SingleCellExperiment object |
| normalizeSCE | Normalise a SingleCellExperiment object using pre-computed size factors |
| normliseExprs | Normalise expression expression levels for an 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 cell phenotype data from an SingleCellExperiment object |
| plotColData | Plot cell phenotype data from an SingleCellExperiment object |
| plotDiffusionMap | Plot a diffusion map for a SingleCellExperiment object |
| plotDiffusionMap-method | Plot a diffusion map for a SingleCellExperiment object |
| plotExplanatoryVariables | Plot explanatory variables ordered by percentage of phenotypic variance explained |
| plotExpression | Plot expression values for a set of features (e.g. genes or transcripts) |
| plotExpression-method | Plot expression values for a set of features (e.g. genes or transcripts) |
| plotExpressionDefault | Plot expression values for a set of features (e.g. genes or transcripts) |
| plotExprsFreqVsMean | Plot frequency of expression against mean expression level |
| plotExprsVsTxLength | Plot expression against transcript length |
| plotFeatureData | Plot feature (gene) data from a SingleCellExperiment object |
| plotHighestExprs | Plot the features with the highest expression values |
| plotMDS | Produce a multidimensional scaling plot for a SingleCellExperiment object |
| plotMDS-method | Produce a multidimensional scaling plot for a SingleCellExperiment object |
| plotMetadata | Plot metadata for cells or features |
| plotPCA | Plot PCA for a SingleCellExperiment object |
| plotPCA-method | Plot PCA for a SingleCellExperiment object |
| plotPCASCE | Plot PCA for a SingleCellExperiment object |
| plotPhenoData | Plot cell phenotype data from an SingleCellExperiment object |
| plotPlatePosition | Plot cells in plate positions |
| plotQC | Produce QC diagnostic plots |
| plotReducedDim | Plot reduced dimension representation of cells |
| plotReducedDim-method | Plot reduced dimension representation of cells |
| plotReducedDimDefault | Plot reduced dimension representation of cells |
| plotRLE | Plot a relative log expression (RLE) plot |
| plotRLE-method | Plot a relative log expression (RLE) plot |
| plotRowData | Plot feature (gene) data from a SingleCellExperiment object |
| plotScater | Plot an overview of expression for each cell |
| plotTSNE | Plot t-SNE for an SingleCellExperiment object |
| plotTSNE-method | Plot t-SNE for an SingleCellExperiment object |
| 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 |
| rename | Rename variables of 'colData(object)'. |
| rename-method | Rename variables of 'colData(object)'. |
| runDiffusionMap | Plot a diffusion map for a SingleCellExperiment object |
| runKallisto | kallisto wrapper functions |
| runPCA | Plot PCA for a SingleCellExperiment object |
| runSalmon | Salmon wrapper functions |
| runTSNE | Plot t-SNE for an SingleCellExperiment object |
| salmon-wrapper | Salmon wrapper functions |
| 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 |
| toCellDataSet | Retrieve a representation of gene expression |
| toSingleCellExperiment | Convert an SCESet object to a SingleCellExperiment object |
| updateSCESet | Convert an SCESet object to a SingleCellExperiment object |