ANOVA                   Analysis of Variance
HC                      Hierarchical Clustering Analysis
PCA                     Principal Component Analysis
addOutlierFromFile      Remove a Set of Samples to the Outlier List
addOutlierFromList      Remove a Set of Samples to the Outlier List
addOutlierFromName      Remove a Sample to the Outlier List
analyzeGeneDetection    Gene Detection Per Sample
applyHC                 Hierarchical Clustering Analysis
applyPCA                Apply a PCA Model to New Expression Data
autoAnalysis            Analyze Expression Data to Obtain
                        Differentially Expressed Genes
boxPlotByGenes          Box Plot by Genes
boxPlotBySamples        Box Plot by Samples
clearExcludedExpDataColumnNames
                        Clear Excluded Column Names for Reading Tab
                        Delimited Linear Exp Data Files
clearExcludedExpDataRowNames
                        Clear Excluded Row Names for Reading Tab
                        Delimited Linear Exp Data Files
clearGeneGroupColorAndSymbols
                        Clear the Customized Sample Group Color and
                        Symbol Settings
clearSampleGroupColorAndSymbols
                        Clear the Customized Sample Group Color and
                        Symbol Settings
clusterPCAScore         Cluster PCA Score
clustertSNE             Cluster tSNE Result
createGeneListFromGeneNames
                        Gene List from Gene Names
display3DPCAScore       3D PCA Score Plot
displayANOVAPValues     Display ANOVA P-Values
displayCorrGenes        Display gene expression profile of co-expressed
                        genes of selected
displayHC               Display Hierarchical Clustering
displayPCAGeneScores    Display PCA Gene Scores
displayPCALoading       PCA Loading Plot
displayPCAScore         PCA Score Plot
displayPCAScree         PCA Scree Plot
displaytSNE             tSNE Plot
excludeExpDataColumnByName
                        Excluded Column Names for Reading Tab Delimited
                        Linear Exp Data Files
excludeExpDataRowByName
                        Excluded Row Names for Reading Tab Delimited
                        Linear Exp Data Files
exportHCHeatmap         Export Hierarchical Clustering Analysis Heatmap
findCorrGenesFromFile   Find Co-Expressed Genes
findCorrGenesFromList   Find Co-Expressed Genes
findCorrGenesFromName   Find Co-Expressed Genes
firstRun                Install Dependent Packages
fluidigmSC              Fluidigm Singular Analysis Toolset v3.6.2
foldChangeAnalysis      Fold Change Analysis Between Two Sample Groups
getGeneClusterByThreshold
                        Obtain Gene Cluster by Threshold
getSampleClusterByThreshold
                        Obtain Sample Cluster by Threshold
getTopANOVAGenes        Get Top ANOVA Genes
getTopPCAGenes          Get Top Ranked PCA Genes
identifyGeneClusters    Identify Gene Clusters
identifyOutliers        Identify Outliers
identifySampleClusters
                        Identify Sample Clusters
mergeExpData            Merge EXP Objects
mergeGeneList           Merge Gene Lists
mergeSampleList         Merge Sample Lists
mergeVariantList        Merge Variant Lists
pairwiseANOVASummary    ANOVA Analysis Summary
pairwiseScatterPlotBetweenSampleGroups
                        Correlation Scatter Plot of Sample Groups
readCtExp               Read Ct Expression Data
readData                Read Data
readExpObject           Read EXP Object Files
readLinearExp           Read Linear Expression Data
readVCF                 Read VCF Data
readVCObject            Read VC Object Files
removeGene              Remove a Gene
removeGeneGroup         Remove a Group of Genes
removeGenesByCtExp      Remove Genes with Low Expression
removeGenesByLinearExp
                        Remove Genes with Low Expression
removeSample            Remove a Sample
removeSampleGroup       Remove a Group of Samples
resetGeneList           Reset Gene List
resetHCMarginFactor     Reset HC Display Margin
resetSampleList         Reset Sample List
restoreAllOutlier       Restore Outliers
restoreOutlierFromList
                        Restore Outliers from an Outlier List
restoreOutlierFromName
                        Restore an Outlier
retainGeneGroup         Retain a Group of Genes
retainSampleGroup       Retain a Group of Samples
saveData                Save Data
scExpFunctions          Quick Help for Singular Expression Analysis
                        Functions
scFunctions             Quick Help for Singular R Functions
scVarFunctions          Quick Help for Singular Variant Analysis
                        Functions
scVariables             Quick Help for Current Variables used in data
                        analysis by Singular package
setGeneGroupColorAndSymbols
                        Customize Gene Group Color and Symbol Settings
setHCMarginFactor       Set HC Display Margin
setSampleGroupColorAndSymbols
                        Customize Sample Group Color and Symbol
                        Settings
summaryExp              Summarize an Expression Object
tSNE                    T-Distributed Stochastic Neighbor Embedding
updateGeneListFromFile
                        Update Gene List
updateGeneListFromList
                        Update Gene List
updateLod               Recalculates the Log2 Expression (Log2EX) with
                        a new LoD.
updateSampleListFromFile
                        Update Sample List
updateSampleListFromList
                        Update Sample List
updateSampleListFromName
                        Update Sample List
vcAddOutlierFromFile    Remove a Set of Samples to the Outlier List
vcAddOutlierFromList    Remove a Set of Samples to the Outlier List
vcAddOutlierFromName    Remove a Sample to the Outlier List
vcAutoAnalysis          Analyze Variant Data via GUI to Obtain Variants
                        of Interest
vcClearSampleGroupColorAndSymbols
                        Clear the Customized Sample Group Color and
                        Symbol Settings
vcClearVariantGroupColorAndSymbols
                        Clear the Customized Variant Group Color and
                        Symbol Settings
vcDisplayFisherTestResults
                        Display Manhattan plot for Fisher test result
                        of variant calls
vcDisplayHC             Display Hierarchical Clustering of Variant Data
vcEvalSampleGroupVariants
                        Evaluate Variant-Calling Performance for Sample
                        Groups
vcEvalSampleVariants    Evaluate Variant-Calling Performance for
                        Individual Samples
vcExportHCHeatmap       Export Heatmap of Hierarchical Clustering
                        Analysis
vcGetCommonVariantListWithCallFromSampleGroup
                        Get Common Variant List with Calls from a
                        Sample Group
vcGetFailVariantsFromVariantCall
                        Get Failed Variants From Variant Call
vcGetFilterVariantListByVariantQuality
                        Get High-Quality Variant List
vcGetPassVariantsFromVariantCall
                        Get Passed Variants From Variant Call
vcGetSignificantVariants
                        Get Significant Variant List in Case-Control
                        Study
vcGetVariantListBySampleGroupAlleleFrequency
                        Get Variant List with Common GT in a Sample
                        Group
vcGetVariantListWithCallFromSample
                        Get Variant List with Calls from a Sample
vcHC                    Hierarchical Clustering Analysis for Variant
                        Data
vcIdentifySampleClusters
                        Identify Sample Clusters
vcIdentifySigVariants   Identify Mutations or Variants at Single-Cell
                        Resolution
vcIdentifyVariantClusters
                        Identify Variant Clusters
vcMergeVCObj            Merge VC Objects
vcPerformFisherTest     Perform Fisher EXACT Test for VC data
vcRemoveLowQualitySamples
                        Remove Low-Quality Samples from Sample List of
                        VC
vcRemoveSampleGroup     Remove a Group of Samples
vcRemoveSamples         Remove a Sample
vcRemoveVariant         Remove a Variant
vcRemoveVariantGroup    Remove a Variant Group
vcResetSampleList       Reset Sample List
vcResetVariantList      Reset Variant List
vcRestoreAllOutlier     Restore All Outliers
vcRestoreOutlierFromList
                        Restore Outliers from an Outlier List
vcRestoreOutlierFromName
                        Restore an Outlier in VC Object
vcRetainSampleGroup     Retain a Group of Samples
vcRetainVariantGroup    Retain a Group of Variants
vcSetSampleGroupColorAndSymbols
                        Customize Sample Group Color and Symbol
                        Settings
vcSetVariantGroupColorAndSymbols
                        Customize Variant Group Color and Symbol
                        Settings
vcUpdateSampleListFromFile
                        Update Sample List
vcUpdateSampleListFromList
                        Update Sample List
vcUpdateSampleListFromName
                        Update Sample List From Sample Name
vcUpdateVariantListByVariantQuality
                        Update VC Object According to its Variant
                        Quality
vcUpdateVariantListFromFile
                        Update Variant List
vcUpdateVariantListFromList
                        Update Variant List
vcUpdateVariantListFromVariantAnnotation
                        Update Variant List from VCF Variant
                        Annotations
vcUpdateVariantQuality
                        Determine Quality of Variant Calls in Samples
violinPlotByGenes       Violin Plot by Genes
violinPlotBySamples     Violin Plot by Samples
writeVCF                Save Variant Data as VCF File
