Files in sanger-pathogens/deago

DEAGO: RNASeq differential expression analysis and GO term enrichment reporter

CHANGELOG.md R/annotate.R R/config.R R/contrasts.R R/deseqAnalysis.R R/general.R R/goAnalysis.R R/importTargets.R R/plotToFile.R R/plot_styles.R R/qcPlots.R R/readCountData.R R/resultsDirectory.R README.md inst/script/generateDeagoDataSet.R man/addAnnotationsToDataSet.Rd man/annotateDataset.Rd man/buildConfig.Rd man/constructDESeqDataset.Rd man/contrastSummary.Rd man/filterGeneIdentifiers.Rd man/formatReadCounts.Rd man/getContrasts.Rd man/getGOidentifiers.Rd man/getGOlist.Rd man/getGeneSymbols.Rd man/getGoSymbols.Rd man/getPrincipalComponents.Rd man/getTopGenes.Rd man/getVennCounts.Rd man/importAnnotation.Rd man/importConfig.Rd man/importTargets.Rd man/labelDEgenes.Rd man/makeResultDir.Rd man/pcaPlot.Rd man/pcaScreePlot.Rd man/pcaSummary.Rd man/plotContrastMA.Rd man/plotCooks.Rd man/plotDensity.Rd man/plotDispersionEstimates.Rd man/plotNullCounts.Rd man/plotReadCounts.Rd man/plotSampleDistances.Rd man/plotToFile.Rd man/plotVenn.Rd man/plotVolcano.Rd man/prepareColData.Rd man/prepareContrast.Rd man/prepareContrastTable.Rd man/prepareGOtable.Rd man/prepareGoData.Rd man/readCountData.Rd man/roundToBase.Rd man/roundToFactorOfTen.Rd man/runDESeqAnalysis.Rd man/runGoAnalysis.Rd man/topGOanalysis.Rd man/validateConfig.Rd man/validateTargets.Rd man/writeConfig.Rd man/writeContrasts.Rd man/writeGOtables.Rd tests/testthat.R tests/testthat/helper-all.R tests/testthat/helper-plots.R tests/testthat/test-annotate.R tests/testthat/test-config.R tests/testthat/test-contrastPlots.R tests/testthat/test-contrasts.R tests/testthat/test-deseqAnalysis.R tests/testthat/test-general.R tests/testthat/test-goAnalysis.R tests/testthat/test-importTargets.R tests/testthat/test-plotToFile.R tests/testthat/test-plot_styles.R tests/testthat/test-qcPlots.R tests/testthat/test-readCountData.R tests/testthat/test-resultsDirectory.R vignettes/deago.Rmd