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A B C F G I M N P R S T U W misc
| scater-package | Single-cell analysis toolkit for expression in R |
| areSizeFactorsCentred | Check if the size factors are centred at unity |
| arrange | Arrange rows of 'pData(object)' by variables. |
| arrange-method | Arrange rows of 'pData(object)' by variables. |
| arrange.SCESet | Arrange rows of 'pData(object)' by variables. |
| bootstraps | Accessor and replacement for bootstrap results in an SCESet object |
| bootstraps-method | Accessor and replacement for bootstrap results in an SCESet object |
| bootstraps.SCESet | Accessor and replacement for bootstrap results in an SCESet object |
| bootstraps<- | Accessor and replacement for bootstrap results in an SCESet object |
| bootstraps<--method | Accessor and replacement for bootstrap results in an SCESet 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) |
| cellDist | cellPairwiseDistances in an SCESet object |
| cellDist-method | cellPairwiseDistances in an SCESet object |
| cellDist<- | cellPairwiseDistances in an SCESet object |
| cellDist<--method | cellPairwiseDistances in an SCESet object |
| cellDistSCESet | cellPairwiseDistances in an SCESet object |
| cellNames | Get or set cell names from an SCESet object |
| cellNames<- | Get or set cell names from an SCESet object |
| cellNames<--method | Get or set cell names from an SCESet object |
| cellPairwiseDistances | cellPairwiseDistances in an SCESet object |
| cellPairwiseDistances-method | cellPairwiseDistances in an SCESet object |
| cellPairwiseDistances.SCESet | cellPairwiseDistances in an SCESet object |
| cellPairwiseDistances<- | cellPairwiseDistances in an SCESet object |
| cellPairwiseDistances<--method | cellPairwiseDistances in an SCESet object |
| counts | Accessors for the 'counts' element of an SCESet object. |
| counts-method | Accessors for the 'counts' element of an SCESet object. |
| counts.SCESet | Accessors for the 'counts' element of an SCESet object. |
| counts<--method | Accessors for the 'counts' element of an SCESet object. |
| cpm | Accessors for the 'cpm' (counts per million) element of an SCESet object. |
| cpm-method | Accessors for the 'cpm' (counts per million) element of an SCESet object. |
| cpm<- | Accessors for the 'cpm' (counts per million) element of an SCESet object. |
| cpm<--method | Accessors for the 'cpm' (counts per million) element of an SCESet object. |
| cpmSCESet | Accessors for the 'cpm' (counts per million) element of an SCESet object. |
| fData | Replaces featureData in an SCESet object |
| fData-method | Replaces featureData in an SCESet object |
| fData<--method | Replaces featureData in an SCESet object |
| featDist | featurePairwiseDistances in an SCESet object |
| featDist-method | featurePairwiseDistances in an SCESet object |
| featDist<- | featurePairwiseDistances in an SCESet object |
| featDist<--method | featurePairwiseDistances in an SCESet object |
| featDistSCESet | featurePairwiseDistances in an SCESet object |
| featureControlInfo | featureControlInfo in an SCESet object |
| featureControlInfo-method | featureControlInfo in an SCESet object |
| featureControlInfo.SCESet | featureControlInfo in an SCESet object |
| featureControlInfo<- | featureControlInfo in an SCESet object |
| featureControlInfo<--method | featureControlInfo in an SCESet object |
| featurePairwiseDistances | featurePairwiseDistances in an SCESet object |
| featurePairwiseDistances-method | featurePairwiseDistances in an SCESet object |
| featurePairwiseDistances<- | featurePairwiseDistances in an SCESet object |
| featurePairwiseDistances<--method | featurePairwiseDistances in an SCESet object |
| featurePairwiseDistancesSCESet | featurePairwiseDistances in an SCESet object |
| filter | Return 'SCESet' with cells matching conditions. |
| filter-method | Return 'SCESet' with cells matching conditions. |
| filter.SCESet | Return 'SCESet' with cells matching conditions. |
| findImportantPCs | Find most important principal components for a given variable |
| fpkm | Accessors for the 'fpkm' (fragments per kilobase of exon per million reads mapped) element of an SCESet object. |
| fpkm-method | Accessors for the 'fpkm' (fragments per kilobase of exon per million reads mapped) element of an SCESet object. |
| fpkm.SCESet | Accessors for the 'fpkm' (fragments per kilobase of exon per million reads mapped) element of an SCESet object. |
| fpkm<- | Accessors for the 'fpkm' (fragments per kilobase of exon per million reads mapped) element of an SCESet object. |
| fpkm<--method | Accessors for the 'fpkm' (fragments per kilobase of exon per million reads mapped) element of an SCESet object. |
| fromCellDataSet | Convert a 'CellDataSet' to an 'SCESet' |
| getBMFeatureAnnos | Get feature annotation information from Biomart |
| getExprs | Retrieve a representation of gene expression |
| get_exprs | Generic accessor for expression data from an SCESet object. |
| get_exprs-method | Generic accessor for expression data from an SCESet object. |
| get_exprs.SCESet | Generic accessor for expression data from an SCESet object. |
| isOutlier | Identify if a cell is an outlier based on a metric |
| isSpike | Get spike-in features in an SCESet object |
| isSpike-method | Get spike-in features in an SCESet object |
| is_exprs | Accessors for the 'is_exprs' element of an SCESet object. |
| is_exprs-method | Accessors for the 'is_exprs' element of an SCESet object. |
| is_exprs.SCESet | Accessors for the 'is_exprs' element of an SCESet object. |
| is_exprs<- | Accessors for the 'is_exprs' element of an SCESet object. |
| is_exprs<--method | Accessors for the 'is_exprs' element of an SCESet object. |
| mergeSCESet | Merge SCESet objects |
| multiplot | Multiple plot function for ggplot2 plots |
| mutate | Add new variables to 'pData(object)'. |
| mutate-method | Add new variables to 'pData(object)'. |
| mutate.SCESet | Add new variables to 'pData(object)'. |
| newSCESet | Create a new SCESet object. |
| nexprs | Count the number of expressed genes per cell |
| normalise | Normalise an SCESet object using pre-computed size factors |
| normalise-method | Normalise an SCESet object using pre-computed size factors |
| normaliseExprs | Normalise expression expression levels for an SCESet object |
| normalize | Normalise an SCESet object using pre-computed size factors |
| normalize-method | Normalise an SCESet object using pre-computed size factors |
| normalize.SCESet | Normalise an SCESet object using pre-computed size factors |
| normalizeExprs | Normalise expression expression levels for an SCESet object |
| normliseExprs | Normalise expression expression levels for an SCESet object |
| norm_counts | Accessors for the 'norm_counts' element of an SCESet object. |
| norm_counts-method | Accessors for the 'norm_counts' element of an SCESet object. |
| norm_counts.SCESet | Accessors for the 'norm_counts' element of an SCESet object. |
| norm_counts<- | Accessors for the 'norm_counts' element of an SCESet object. |
| norm_counts<--method | Accessors for the 'norm_counts' element of an SCESet object. |
| norm_cpm | Accessors for the 'norm_cpm' (normalised counts per million) element of an SCESet object. |
| norm_cpm-method | Accessors for the 'norm_cpm' (normalised counts per million) element of an SCESet object. |
| norm_cpm.SCESet | Accessors for the 'norm_cpm' (normalised counts per million) element of an SCESet object. |
| norm_cpm<- | Accessors for the 'norm_cpm' (normalised counts per million) element of an SCESet object. |
| norm_cpm<--method | Accessors for the 'norm_cpm' (normalised counts per million) element of an SCESet object. |
| norm_exprs | Accessors for the 'norm_exprs' (normalised expression) element of an SCESet object. |
| norm_exprs-method | Accessors for the 'norm_exprs' (normalised expression) element of an SCESet object. |
| norm_exprs.SCESet | Accessors for the 'norm_exprs' (normalised expression) element of an SCESet object. |
| norm_exprs<- | Accessors for the 'norm_exprs' (normalised expression) element of an SCESet object. |
| norm_exprs<--method | Accessors for the 'norm_exprs' (normalised expression) element of an SCESet object. |
| norm_fpkm | Accessors for the 'norm_fpkm' (normalised fragments per kilobase of exon per million reads mapped) element of an SCESet object. |
| norm_fpkm-method | Accessors for the 'norm_fpkm' (normalised fragments per kilobase of exon per million reads mapped) element of an SCESet object. |
| norm_fpkm.SCESet | Accessors for the 'norm_fpkm' (normalised fragments per kilobase of exon per million reads mapped) element of an SCESet object. |
| norm_fpkm<- | Accessors for the 'norm_fpkm' (normalised fragments per kilobase of exon per million reads mapped) element of an SCESet object. |
| norm_fpkm<--method | Accessors for the 'norm_fpkm' (normalised fragments per kilobase of exon per million reads mapped) element of an SCESet object. |
| norm_tpm | Accessors for the 'norm_tpm' (transcripts per million) element of an SCESet object. |
| norm_tpm-method | Accessors for the 'norm_tpm' (transcripts per million) element of an SCESet object. |
| norm_tpm.SCESet | Accessors for the 'norm_tpm' (transcripts per million) element of an SCESet object. |
| norm_tpm<- | Accessors for the 'norm_tpm' (transcripts per million) element of an SCESet object. |
| norm_tpm<--method | Accessors for the 'norm_tpm' (transcripts per million) element of an SCESet object. |
| pData | Replaces phenoData in an SCESet object |
| pData-method | Replaces phenoData in an SCESet object |
| pData<--method | Replaces phenoData in an SCESet object |
| plot | Plot an overview of expression for each cell |
| plot-method | Plot an overview of expression for each cell |
| plotDiffusionMap | Plot a diffusion map for an SCESet object |
| plotDiffusionMap-method | Plot a diffusion map for an SCESet object |
| plotDiffusionMapSCESet | Plot a diffusion map for an SCESet 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) |
| plotExpressionSCESet | 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 an SCESet object |
| plotHighestExprs | Plot the features with the highest expression values |
| plotMDS | Produce a multidimensional scaling plot for an SCESet object |
| plotMDS-method | Produce a multidimensional scaling plot for an SCESet object |
| plotMDSSCESet | Produce a multidimensional scaling plot for an SCESet object |
| plotMetadata | Plot metadata for cells or features |
| plotPCA | Plot PCA for an SCESet object |
| plotPCA-method | Plot PCA for an SCESet object |
| plotPCASCESet | Plot PCA for an SCESet object |
| plotPhenoData | Plot phenotype data from an SCESet object |
| plotPlatePosition | Plot cells in plate positions |
| plotQC | Produce QC diagnostic plots |
| plotReducedDIm | Plot reduced dimension representation of cells |
| plotReducedDim | Plot reduced dimension representation of cells |
| plotReducedDim-method | Plot reduced dimension representation of cells |
| plotReducedDim.default | Plot reduced dimension representation of cells |
| plotReducedDim.SCESet | Plot reduced dimension representation of cells |
| plotRLE | Plot a relative log expression (RLE) plot |
| plotRLE-method | Plot a relative log expression (RLE) plot |
| plotSCESet | Plot an overview of expression for each cell |
| plotTSNE | Plot t-SNE for an SCESet object |
| plotTSNE-method | Plot t-SNE for an SCESet object |
| read10XResults | Load in data from 10X experiment |
| readKallistoResults | Read kallisto results from a batch of jobs |
| readKallistoResultsOneSample | Read kallisto results for a single sample into a list |
| readSalmonResults | Read Salmon results from a batch of jobs |
| readSalmonResultsOneSample | Read Salmon results for a single sample into a list |
| readTxResults | Read transcript quantification data with tximport package |
| redDim | Reduced dimension representation for cells in an SCESet object |
| redDim-method | Reduced dimension representation for cells in an SCESet object |
| redDim.SCESet | Reduced dimension representation for cells in an SCESet object |
| redDim<- | Reduced dimension representation for cells in an SCESet object |
| redDim<--method | Reduced dimension representation for cells in an SCESet object |
| reducedDimension | Reduced dimension representation for cells in an SCESet object |
| reducedDimension-method | Reduced dimension representation for cells in an SCESet object |
| reducedDimension.SCESet | Reduced dimension representation for cells in an SCESet object |
| reducedDimension<- | Reduced dimension representation for cells in an SCESet object |
| reducedDimension<--method | Reduced dimension representation for cells in an SCESet object |
| rename | Rename variables of 'pData(object)'. |
| rename-method | Rename variables of 'pData(object)'. |
| rename.SCESet | Rename variables of 'pData(object)'. |
| runKallisto | Run kallisto on FASTQ files to quantify feature abundance |
| runSalmon | Run Salmon on FASTQ files to quantify feature abundance |
| scater_gui | scater GUI function |
| SCESet | The "Single Cell Expression Set" (SCESet) class |
| SCESet-class | The "Single Cell Expression Set" (SCESet) class |
| SCESet-subset | Subsetting SCESet Objects |
| 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 |
| setSpike | Set spike-in features in an SCESet object |
| setSpike<- | Set spike-in features in an SCESet object |
| setSpike<--method | Set spike-in features in an SCESet object |
| set_exprs | Assignment method for the new elements of an SCESet object. |
| set_exprs<- | Assignment method for the new elements of an SCESet object. |
| set_exprs<--method | Assignment method for the new elements of an SCESet object. |
| sizeFactors | Accessors size factors of an SCESet object. |
| sizeFactors-method | Accessors size factors of an SCESet object. |
| sizeFactors.SCESet | Accessors size factors of an SCESet object. |
| sizeFactors<- | Accessors size factors of an SCESet object. |
| sizeFactors<--method | Accessors size factors of an SCESet object. |
| spikes | Extract expression values for spike-in features in an SCESet object |
| spikes-method | Extract expression values for spike-in features in an SCESet object |
| stand_exprs | Accessors for the 'stand_exprs' (standardised expression) element of an SCESet object. |
| stand_exprs-method | Accessors for the 'stand_exprs' (standardised expression) element of an SCESet object. |
| stand_exprs.SCESet | Accessors for the 'stand_exprs' (standardised expression) element of an SCESet object. |
| stand_exprs<- | Accessors for the 'stand_exprs' (standardised expression) element of an SCESet object. |
| stand_exprs<--method | Accessors for the 'stand_exprs' (standardised expression) element of an SCESet object. |
| summariseExprsAcrossFeatures | Summarise expression values across feature |
| toCellDataSet | Convert an 'SCESet' to a 'CellDataSet' |
| tpm | Accessors for the 'tpm' (transcripts per million) element of an SCESet object. |
| tpm-method | Accessors for the 'tpm' (transcripts per million) element of an SCESet object. |
| tpm.SCESet | Accessors for the 'tpm' (transcripts per million) element of an SCESet object. |
| tpm<- | Accessors for the 'tpm' (transcripts per million) element of an SCESet object. |
| tpm<--method | Accessors for the 'tpm' (transcripts per million) element of an SCESet object. |
| updateSCESet | Update an SCESet object to the current version |
| whichSpike | Identify spike-in feature control sets in an SCESet object |
| whichSpike-method | Identify spike-in feature control sets in an SCESet object |
| writeSCESet | Write an SCESet object to an HDF5 file |
| [-method | Subsetting SCESet Objects |