MitoGenes               List of mitochondrial genes of multiple
                        reference
SEG                     Stably Expressed Gene (SEG) list obect, with
                        SEG sets for human and mouse.
calcEffectSizes         Finds the effect sizes for all genes in the
                        original dataset, regardless of significance.
combineSCE              Combine a list of SingleCellExperiment objects
                        as one SingleCellExperiment object
computeHeatmap          Computes heatmap for a set of features against
                        dimensionality reduction components
computeZScore           Compute Z-Score
constructSCE            Create SingleCellExperiment object from csv or
                        txt input
convertSCEToSeurat      convertSCEToSeurat Converts sce object to
                        seurat while retaining all assays and metadata
convertSeuratToSCE      convertSeuratToSCE Converts the input seurat
                        object to a sce object
dedupRowNames           Deduplicate the rownames of a matrix or
                        SingleCellExperiment object
detectCellOutlier       Detecting outliers within the
                        SingleCellExperiment object.
diffAbundanceFET        Calculate Differential Abundance with FET
discreteColorPalette    Generate given number of color codes
distinctColors          Generate a distinct palette for coloring
                        different clusters
downSampleCells         Estimate numbers of detected genes,
                        significantly differentially expressed genes,
                        and median significant effect size
downSampleDepth         Estimate numbers of detected genes,
                        significantly differentially expressed genes,
                        and median significant effect size
expData                 expData Get data item from an input
                        'SingleCellExperiment' object. The data item
                        can be an 'assay', 'altExp' (subset) or a
                        'reducedDim', which is retrieved based on the
                        name of the data item.
expData,ANY,character-method
                        expData Get data item from an input
                        'SingleCellExperiment' object. The data item
                        can be an 'assay', 'altExp' (subset) or a
                        'reducedDim', which is retrieved based on the
                        name of the data item.
expData<-               expData Store data items using tags to identify
                        the type of data item stored. To be used as a
                        replacement for assay<- setter function but
                        with additional parameter to set a tag to a
                        data item.
expData<-,ANY,character,CharacterOrNullOrMissing,logical-method
                        expData Store data items using tags to identify
                        the type of data item stored. To be used as a
                        replacement for assay<- setter function but
                        with additional parameter to set a tag to a
                        data item.
expDataNames            expDataNames Get names of all the data items in
                        the input 'SingleCellExperiment' object
                        including assays, altExps and reducedDims.
expDataNames,ANY-method
                        expDataNames Get names of all the data items in
                        the input 'SingleCellExperiment' object
                        including assays, altExps and reducedDims.
expDeleteDataTag        expDeleteDataTag Remove tag against an input
                        data from the stored tag information in the
                        metadata of the input object.
expSetDataTag           expSetDataTag Set tag to an assay or a data
                        item in the input SCE object.
expTaggedData           expTaggedData Returns a list of names of data
                        items from the input 'SingleCellExperiment'
                        object based upon the input parameters.
exportSCE               Export data in SingleCellExperiment object
exportSCEToSeurat       Export data in Seurat object
exportSCEtoAnnData      Export a SingleCellExperiment R object as
                        Python annData object
exportSCEtoFlatFile     Export a SingleCellExperiment object to flat
                        text files
featureIndex            Retrieve row index for a set of features
generateHTANMeta        Generate HTAN manifest file for droplet and
                        cell count data
generateMeta            Generate HTAN manifest file for droplet and
                        cell count data
generateSimulatedData   Generates a single simulated dataset,
                        bootstrapping from the input counts matrix.
getBiomarker            Given a list of genes and a
                        SingleCellExperiment object, return the binary
                        or continuous expression of the genes.
getDEGTopTable          Get Top Table of a DEG analysis
getDiffAbundanceResults
                        Get/Set diffAbundanceFET result table
getEnrichRResult<-      Get or Set EnrichR Result
getFindMarkerTopTable   Fetch the table of top markers that pass the
                        filtering
getGenesetNamesFromCollection
                        List geneset names from geneSetCollection
getMSigDBTable          Shows MSigDB categories
getPathwayResultNames   List pathway analysis result names
getSampleSummaryStatsTable
                        Stores and returns table of SCTK QC outputs to
                        metadata.
getSceParams            Extract QC parameters from the
                        SingleCellExperiment object
getSeuratVariableFeatures
                        Get variable feature names after running
                        runSeuratFindHVG function
getSoupX<-              Get or Set SoupX Result
getTSCANResults         getTSCANResults accessor function
getTopHVG               Get or set top HVG after calculation
importAlevin            Construct SCE object from Salmon-Alevin output
importAnnData           Create a SingleCellExperiment Object from
                        Python AnnData .h5ad files
importBUStools          Construct SCE object from BUStools output
importCellRanger        Construct SCE object from Cell Ranger output
importCellRangerV2Sample
                        Construct SCE object from Cell Ranger V2 output
                        for a single sample
importCellRangerV3Sample
                        Construct SCE object from Cell Ranger V3 output
                        for a single sample
importDropEst           Create a SingleCellExperiment Object from
                        DropEst output
importExampleData       Retrieve example datasets
importFromFiles         Create a SingleCellExperiment object from files
importGeneSetsFromCollection
                        Imports gene sets from a GeneSetCollection
                        object
importGeneSetsFromGMT   Imports gene sets from a GMT file
importGeneSetsFromList
                        Imports gene sets from a list
importGeneSetsFromMSigDB
                        Imports gene sets from MSigDB
importMitoGeneSet       Import mitochondrial gene sets
importMultipleSources   Imports samples from different sources and
                        compiles them into a list of SCE objects
importOptimus           Construct SCE object from Optimus output
importSEQC              Construct SCE object from seqc output
importSTARsolo          Construct SCE object from STARsolo outputs
iterateSimulations      Returns significance data from a snapshot.
listSampleSummaryStatsTables
                        Lists the table of SCTK QC outputs stored
                        within the metadata.
mergeSCEColData         Merging colData from two singleCellExperiment
                        objects
mouseBrainSubsetSCE     Example Single Cell RNA-Seq data in
                        SingleCellExperiment Object, GSE60361 subset
msigdb_table            MSigDB gene get Category table
plotBarcodeRankDropsResults
                        Plots for runBarcodeRankDrops outputs.
plotBarcodeRankScatter
                        Plots for runBarcodeRankDrops outputs.
plotBatchCorrCompare    Plot comparison of batch corrected result
                        against original assay
plotBatchVariance       Plot the percent of the variation that is
                        explained by batch and condition in the data
plotBcdsResults         Plots for runBcds outputs.
plotClusterAbundance    Plot the differential Abundance
plotCxdsResults         Plots for runCxds outputs.
plotDEGHeatmap          Heatmap visualization of DEG result
plotDEGRegression       Create linear regression plot to show the
                        expression the of top DEGs
plotDEGViolin           Generate violin plot to show the expression of
                        top DEGs
plotDEGVolcano          Generate volcano plot for DEGs
plotDecontXResults      Plots for runDecontX outputs.
plotDimRed              Plot dimensionality reduction from computed
                        metrics including PCA, ICA, tSNE and UMAP
plotDoubletFinderResults
                        Plots for runDoubletFinder outputs.
plotEmptyDropsResults   Plots for runEmptyDrops outputs.
plotEmptyDropsScatter   Plots for runEmptyDrops outputs.
plotFindMarkerHeatmap   Plot a heatmap to visualize the result of
                        'runFindMarker'
plotMASTThresholdGenes
                        MAST Identify adaptive thresholds
plotPCA                 Plot PCA run data from its components.
plotPathway             Generate violin plots for pathway analysis
                        results
plotRunPerCellQCResults
                        Plots for runPerCellQC outputs.
plotSCEBarAssayData     Bar plot of assay data.
plotSCEBarColData       Bar plot of colData.
plotSCEBatchFeatureMean
                        Plot mean feature value in each batch of a
                        SingleCellExperiment object
plotSCEDensity          Density plot of any data stored in the
                        SingleCellExperiment object.
plotSCEDensityAssayData
                        Density plot of assay data.
plotSCEDensityColData   Density plot of colData.
plotSCEDimReduceColData
                        Dimension reduction plot tool for colData
plotSCEDimReduceFeatures
                        Dimension reduction plot tool for assay data
plotSCEHeatmap          Plot heatmap of using data stored in
                        SingleCellExperiment Object
plotSCEScatter          Dimension reduction plot tool for all types of
                        data
plotSCEViolin           Violin plot of any data stored in the
                        SingleCellExperiment object.
plotSCEViolinAssayData
                        Violin plot of assay data.
plotSCEViolinColData    Violin plot of colData.
plotScDblFinderResults
                        Plots for runScDblFinder outputs.
plotScdsHybridResults   Plots for runCxdsBcdsHybrid outputs.
plotScrubletResults     Plots for runScrublet outputs.
plotSeuratElbow         plotSeuratElbow Computes the plot object for
                        elbow plot from the pca slot in the input sce
                        object
plotSeuratGenes         Compute and plot visualizations for marker
                        genes
plotSeuratHVG           plotSeuratHVG Plot highly variable genes from
                        input sce object (must have highly variable
                        genes computations stored)
plotSeuratHeatmap       plotSeuratHeatmap Modifies the heatmap plot
                        object so it contains specified number of
                        heatmaps in a single plot
plotSeuratJackStraw     plotSeuratJackStraw Computes the plot object
                        for jackstraw plot from the pca slot in the
                        input sce object
plotSeuratReduction     plotSeuratReduction Plots the selected
                        dimensionality reduction method
plotSoupXResults        Plot SoupX Result
plotTSCANClusterDEG     Plot features identified by
                        'runTSCANClusterDEAnalysis' on cell 2D
                        embedding with MST overlaid
plotTSCANClusterPseudo
                        Plot TSCAN pseudotime rooted from given cluster
plotTSCANDimReduceFeatures
                        Plot feature expression on cell 2D embedding
                        with MST overlaid
plotTSCANPseudotimeGenes
                        Plot expression changes of top features along a
                        TSCAN pseudotime path
plotTSCANPseudotimeHeatmap
                        Plot heatmap of genes with expression change
                        along TSCAN pseudotime
plotTSCANResults        Plot MST pseudotime values on cell 2D embedding
plotTSNE                Plot t-SNE plot on dimensionality reduction
                        data run from t-SNE method.
plotTopHVG              Plot highly variable genes
plotUMAP                Plot UMAP results either on already run results
                        or run first and then plot.
qcInputProcess          Create SingleCellExperiment object from command
                        line input arguments
readSingleCellMatrix    Read single cell expression matrix
reportCellQC            Get runCellQC .html report
reportClusterAbundance
                        Get plotClusterAbundance .html report
reportDiffAbundanceFET
                        Get diffAbundanceFET .html report
reportDiffExp           Get runDEAnalysis .html report
reportDropletQC         Get runDropletQC .html report
reportFindMarker        Get runFindMarker .html report
reportQCTool            Get .html report of the output of the selected
                        QC algorithm
reportSeurat            Generates an HTML report for the complete
                        Seurat workflow and returns the SCE object with
                        the results computed and stored inside the
                        object.
reportSeuratClustering
                        Generates an HTML report for Seurat Clustering
                        and returns the SCE object with the results
                        computed and stored inside the object.
reportSeuratDimRed      Generates an HTML report for Seurat
                        Dimensionality Reduction and returns the SCE
                        object with the results computed and stored
                        inside the object.
reportSeuratFeatureSelection
                        Generates an HTML report for Seurat Feature
                        Selection and returns the SCE object with the
                        results computed and stored inside the object.
reportSeuratMarkerSelection
                        Generates an HTML report for Seurat Results
                        (including Clustering & Marker Selection) and
                        returns the SCE object with the results
                        computed and stored inside the object.
reportSeuratNormalization
                        Generates an HTML report for Seurat
                        Normalization and returns the SCE object with
                        the results computed and stored inside the
                        object.
reportSeuratResults     Generates an HTML report for Seurat Results
                        (including Clustering & Marker Selection) and
                        returns the SCE object with the results
                        computed and stored inside the object.
reportSeuratRun         Generates an HTML report for Seurat Run
                        (including Normalization, Feature Selection,
                        Dimensionality Reduction & Clustering) and
                        returns the SCE object with the results
                        computed and stored inside the object.
reportSeuratScaling     Generates an HTML report for Seurat Scaling and
                        returns the SCE object with the results
                        computed and stored inside the object.
retrieveSCEIndex        Retrieve cell/feature index by giving
                        identifiers saved in col/rowData
runBBKNN                Apply BBKNN batch effect correction method to
                        SingleCellExperiment object
runBarcodeRankDrops     Identify empty droplets using barcodeRanks.
runBcds                 Find doublets/multiplets using bcds.
runCellQC               Perform comprehensive single cell QC
runComBatSeq            Apply ComBat-Seq batch effect correction method
                        to SingleCellExperiment object
runCxds                 Find doublets/multiplets using cxds.
runCxdsBcdsHybrid       Find doublets/multiplets using
                        cxds_bcds_hybrid.
runDEAnalysis           Perform differential expression analysis on SCE
                        object
runDecontX              Detecting contamination with DecontX.
runDimReduce            Generic Wrapper function for running
                        dimensionality reduction
runDoubletFinder        Generates a doublet score for each cell via
                        doubletFinder
runDropletQC            Perform comprehensive droplet QC
runEmptyDrops           Identify empty droplets using emptyDrops.
runEnrichR              Run EnrichR on SCE object
runFastMNN              Apply a fast version of the mutual nearest
                        neighbors (MNN) batch effect correction method
                        to SingleCellExperiment object
runFeatureSelection     Run Variable Feature Detection Methods
runFindMarker           Find the marker gene set for each cluster
runGSVA                 Run GSVA analysis on a SingleCellExperiment
                        object
runHarmony              Apply Harmony batch effect correction method to
                        SingleCellExperiment object
runKMeans               Get clustering with KMeans
runLimmaBC              Apply Limma's batch effect correction method to
                        SingleCellExperiment object
runMNNCorrect           Apply the mutual nearest neighbors (MNN) batch
                        effect correction method to
                        SingleCellExperiment object
runModelGeneVar         Calculate Variable Genes with Scran
                        modelGeneVar
runNormalization        Run normalization/transformation with various
                        methods
runPerCellQC            Wrapper for calculating QC metrics with scater.
runSCANORAMA            Apply the mutual nearest neighbors (MNN) batch
                        effect correction method to
                        SingleCellExperiment object
runSCMerge              Apply scMerge batch effect correction method to
                        SingleCellExperiment object
runScDblFinder          Detect doublet cells using scDblFinder.
runScranSNN             Get clustering with SNN graph
runScrublet             Find doublets using 'scrublet'.
runSeuratFindClusters   runSeuratFindClusters Computes the clusters
                        from the input sce object and stores them back
                        in sce object
runSeuratFindHVG        runSeuratFindHVG Find highly variable genes and
                        store in the input sce object
runSeuratFindMarkers    runSeuratFindMarkers
runSeuratHeatmap        runSeuratHeatmap Computes the heatmap plot
                        object from the pca slot in the input sce
                        object
runSeuratICA            runSeuratICA Computes ICA on the input sce
                        object and stores the calculated independent
                        components within the sce object
runSeuratIntegration    runSeuratIntegration A wrapper function to
                        Seurat Batch-Correction/Integration workflow.
runSeuratJackStraw      runSeuratJackStraw Compute jackstraw plot and
                        store the computations in the input sce object
runSeuratNormalizeData
                        runSeuratNormalizeData Wrapper for
                        NormalizeData() function from seurat library
                        Normalizes the sce object according to the
                        input parameters
runSeuratPCA            runSeuratPCA Computes PCA on the input sce
                        object and stores the calculated principal
                        components within the sce object
runSeuratSCTransform    runSeuratSCTransform Runs the SCTransform
                        function to transform/normalize the input data
runSeuratScaleData      runSeuratScaleData Scales the input sce object
                        according to the input parameters
runSeuratTSNE           runSeuratTSNE Computes tSNE from the given sce
                        object and stores the tSNE computations back
                        into the sce object
runSeuratUMAP           runSeuratUMAP Computes UMAP from the given sce
                        object and stores the UMAP computations back
                        into the sce object
runSingleR              Label cell types with SingleR
runSoupX                Detecting and correct contamination with SoupX
runTSCAN                Run TSCAN to obtain pseudotime values for cells
runTSCANClusterDEAnalysis
                        Find DE genes between all TSCAN paths rooted
                        from given cluster
runTSCANDEG             Test gene expression changes along a TSCAN
                        trajectory path
runTSNE                 Run t-SNE embedding with Rtsne method
runUMAP                 Run UMAP embedding with scater method
runVAM                  Run VAM to score gene sets in single cell data
runZINBWaVE             Apply ZINBWaVE Batch effect correction method
                        to SingleCellExperiment object
sampleSummaryStats      Generate table of SCTK QC outputs.
scaterCPM               scaterCPM Uses CPM from scater library to
                        compute counts-per-million.
scaterPCA               Perform scater PCA on a SingleCellExperiment
                        Object
scaterlogNormCounts     scaterlogNormCounts Uses logNormCounts to log
                        normalize input data
sce                     Example Single Cell RNA-Seq data in
                        SingleCellExperiment Object, subset of 10x
                        public dataset
sceBatches              Example Single Cell RNA-Seq data in
                        SingleCellExperiment object, with different
                        batches annotated
sctkListGeneSetCollections
                        Lists imported GeneSetCollections
sctkPythonInstallConda
                        Installs Python packages into a Conda
                        environment
sctkPythonInstallVirtualEnv
                        Installs Python packages into a virtual
                        environment
selectSCTKConda         Selects a Conda environment
selectSCTKVirtualEnvironment
                        Selects a virtual environment
setRowNames             Set rownames of SCE with a character vector or
                        a rowData column
setSCTKDisplayRow       Indicates which rowData to use for
                        visualization
singleCellTK            Run the single cell analysis app
subDiffEx               Passes the output of generateSimulatedData() to
                        differential expression tests, picking either
                        t-tests or ANOVA for data with only two
                        conditions or multiple conditions,
                        respectively.
subsetSCECols           Subset a SingleCellExperiment object by columns
subsetSCERows           Subset a SingleCellExperiment object by rows
summarizeSCE            Summarize an assay in a SingleCellExperiment
trimCounts              Trim Counts
