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A B C D E F G H I M P R S T U V W
| 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 |
| ANOVA | Analysis of Variance |
| 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 |
| HC | Hierarchical Clustering Analysis |
| 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 |
| PCA | Principal Component Analysis |
| 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 |