ComBatSCE               ComBatSCE
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
MAST                    MAST
SCtkExperiment          Create a SCtkExperiment
SCtkExperiment-class    A lightweight S4 extension to the
                        SingleCellExperiment class to store additional
                        information.
alignSingleCellData     Align Single Cell RNA-Seq Data and Create a
                        SCtkExperiment Object
calcEffectSizes         Finds the effect sizes for all genes in the
                        original dataset, regardless of significance.
convertGeneIDs          Convert Gene IDs
createSCE               Create a SCtkExperiment object
distinctColors          Generate a distinct palette for coloring
                        different clusters
enrichRSCE              enrichR Given a list of genes this function
                        runs the enrichR() to perform Gene enrichment
filterSCData            Filter Genes and Samples from a Single Cell
                        Object
generateSimulatedData   Generates a single simulated dataset,
                        bootstrapping from the input counts matrix.
getBiomarker            Given a list of genes and a SCtkExperiment
                        object, return the binary or continuous
                        expression of the genes.
getClusterInputData     Get data to use as input clustering algorithms
getPCA                  Get and plot PCA components for a SCtkE object
getTSNE                 Run t-SNE dimensionality reduction method on
                        the assay data.
getUMAP                 Uniform Manifold Approximation and
                        Projection(UMAP) algorithm for dimension
                        reduction.
gsvaSCE                 Run GSVA analysis on a SCtkExperiment object.
iterateSimulations      Returns significance data from a snapshot.
mouseBrainSubsetSCE     Example Single Cell RNA-Seq data in
                        SCtkExperiment Object, GSE60361 subset
parseRsubreadLogs       Parse Rsubread Logs for Mapping and Feature
                        Count Statistics
pcaVariances            Get PCA variances
pcaVariances<-          Set PCA variances
plotBatchVariance       Plot the percent of the variation that is
                        explained by batch and condition in the data
plotBiomarker           Given a set of genes, return a ggplot of
                        expression values.
plotDiffEx              Plot Differential Expression
plotPCA                 Plot PCA run data from its components.
plotTSNE                Plot t-SNE plot on dimensionality reduction
                        data run from t-SNE method.
plotUMAP                Plot UMAP results either on already run results
                        or run first and then plot.
saveBiomarkerRes        saveBiomarkerRes Save biomarker gene
                        information with a custom name when provided
                        with diffex results.
saveDiffExResults       saveDiffExResults Save Differential Expression
                        Results with a custom name.
scDiffEx                Perform differential expression analysis on a
                        SCtkExperiment object
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.
summarizeTable          Summarize SCtkExperiment
visPlot                 visPlot
