Man pages for sanger-pathogens/deago
DEAGO: RNASeq differential expression analysis and GO term enrichment reporter
| addAnnotationsToDataSet | Add Annotations To DESeqDataSet |
| annotateDataset | Annotate DESeqDataSet |
| buildConfig | Build Configuration File |
| constructDESeqDataset | Construct DESeq2 dataset |
| contrastSummary | Differential expression summary |
| filterGeneIdentifiers | Filter DE gene identifiers in GO term |
| formatReadCounts | Format count matrix from DESeqDataSet |
| getContrasts | Extract contrasts from DESeq2 results |
| getGeneSymbols | Extract Gene Symbols |
| getGOidentifiers | Get gene identifiers for GO terms |
| getGOlist | Transform Delimited GO Terms To List |
| getGoSymbols | Get gene symbols for GO terms |
| getPrincipalComponents | Calculate principal components |
| getTopGenes | Subset top DE genes |
| getVennCounts | Generate count matrix for venn diagram |
| importAnnotation | Import Annotation File |
| importConfig | Read Configuration File |
| importTargets | Read Targets File |
| labelDEgenes | Label DE genes |
| makeResultDir | Make Results Directory |
| pcaPlot | PCA Plot |
| pcaScreePlot | PCA Scree Plot |
| pcaSummary | PCA Summary |
| plotContrastMA | Contrast MA plot |
| plotCooks | Plot Cook's Distances |
| plotDensity | Plot density |
| plotDispersionEstimates | Plot Dispersion Estimates |
| plotNullCounts | Plot Null Counts |
| plotReadCounts | Plot Read Counts |
| plotSampleDistances | Plot Sample Distances |
| plotToFile | Write Plot To File |
| plotVenn | Venn diagram |
| plotVolcano | Volcano plot |
| prepareColData | Construct input matrix for DESeq2 |
| prepareContrast | Prepares contrasts table for writing |
| prepareContrastTable | Prepare contrast table |
| prepareGoData | Prepare GO data |
| prepareGOtable | Prepare GO results datatable |
| readCountData | Read Count Data |
| roundToBase | Round To Base |
| roundToFactorOfTen | Round Factor Ten |
| runDESeqAnalysis | Differential expression analysis using DESeq2 |
| runGoAnalysis | GO enrichment analysis |
| topGOanalysis | Run topGO analysis |
| validateConfig | Validate Parameter List |
| validateTargets | Validate Targets File |
| writeConfig | Write Configuration File |
| writeContrasts | Extract contrasts from DESeq2 results |
| writeGOtables | Write GO results table to file |
