Man pages for dynverse/scaterlegacy
Single-cell analysis toolkit for gene expression data in R
| areSizeFactorsCentred | Check if the size factors are centred at unity |
| arrange | Arrange rows of 'pData(object)' by variables. |
| bootstraps | Accessor and replacement for bootstrap results in an SCESet... |
| calcAverage | Calculate average counts, adjusting for size factors or... |
| calcIsExprs | Calculate which features are expressed in which cells using a... |
| 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) |
| cellNames | Get or set cell names from an SCESet object |
| cellPairwiseDistances | cellPairwiseDistances in an SCESet object |
| counts | Accessors for the 'counts' element of an SCESet object. |
| cpm | Accessors for the 'cpm' (counts per million) element of an... |
| fData | Replaces featureData in an SCESet object |
| featureControlInfo | featureControlInfo in an SCESet object |
| featurePairwiseDistances | featurePairwiseDistances in an SCESet object |
| filter | 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... |
| fromCellDataSet | Convert a 'CellDataSet' to an 'SCESet' |
| getBMFeatureAnnos | Get feature annotation information from Biomart |
| get_exprs | Generic accessor for expression data from an SCESet object. |
| getExprs | Retrieve a representation of gene expression |
| is_exprs | Accessors for the 'is_exprs' element of an SCESet object. |
| isOutlier | Identify if a cell is an outlier based on a metric |
| isSpike | Get spike-in features in an SCESet object |
| mergeSCESet | Merge SCESet objects |
| multiplot | Multiple plot function for ggplot2 plots |
| mutate | Add new variables to 'pData(object)'. |
| newSCESet | Create a new SCESet object. |
| nexprs | Count the number of expressed genes per cell |
| normaliseExprs | Normalise expression expression levels for an SCESet object |
| normalize | Normalise an SCESet object using pre-computed size factors |
| norm_counts | Accessors for the 'norm_counts' element of an SCESet object. |
| norm_cpm | Accessors for the 'norm_cpm' (normalised counts per million)... |
| norm_exprs | Accessors for the 'norm_exprs' (normalised expression)... |
| norm_fpkm | Accessors for the 'norm_fpkm' (normalised fragments per... |
| norm_tpm | Accessors for the 'norm_tpm' (transcripts per million)... |
| pData | Replaces phenoData in an SCESet object |
| plot | Plot an overview of expression for each cell |
| plotDiffusionMap | Plot a diffusion map for an SCESet object |
| plotExplanatoryVariables | Plot explanatory variables ordered by percentage of... |
| plotExpression | Plot expression values for a set of features (e.g. genes or... |
| 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 |
| plotMetadata | Plot metadata for cells or features |
| plotPCA | 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 |
| plotRLE | Plot a relative log expression (RLE) plot |
| plotTSNE | 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 |
| reducedDimension | Reduced dimension representation for cells in an SCESet... |
| rename | 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 |
| scaterlegacy-package | Single-cell analysis toolkit for expression in R |
| SCESet | 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... |
| sc_example_counts | A small example of single-cell counts dataset to demonstrate... |
| set_exprs | Assignment method for the new elements of an SCESet object. |
| setSpike | Set spike-in features in an SCESet object |
| sizeFactors | Accessors size factors of an SCESet object. |
| spikes | Extract expression values for spike-in features in an SCESet... |
| stand_exprs | Accessors for the 'stand_exprs' (standardised expression)... |
| summariseExprsAcrossFeatures | Summarise expression values across feature |
| toCellDataSet | Convert an 'SCESet' to a 'CellDataSet' |
| tpm | Accessors for the 'tpm' (transcripts per million) element of... |
| updateSCESet | Update an SCESet object to the current version |
| whichSpike | Identify spike-in feature control sets in an SCESet object |
| writeSCESet | Write an SCESet object to an HDF5 file |
