Files in microresearcher/MicroVis

Microbiome Analysis and Visualization

R/ASVtoTaxa.R R/analysisAldex.R R/analysisAlphaDiv.R R/analysisBetaDiv.R R/analysisClusterSamples.R R/analysisDeseq.R R/analysisFeatureCorr.R R/analysisFoldChange.R R/analysisLMEM.R R/analysisLefse.R R/analysisNetwork.R R/analysisPairedCor.R R/analysisPermanova.R R/analysisRF-Boruta.R R/analysisUnivar.R R/cclasso.R R/changeFactor.R R/checkGroups.R R/chooseFactors.R R/colorGroups.R R/combineDatasets.R R/datasetTranslations.R R/dsState.R R/excludeFeatures.R R/featureFiltering.R R/ftRatios.R R/ggcorrplot_functions.R R/inspectDataset.R R/loadFunctionalData.R R/loadMetadata.R R/loadTaxonomy.R R/makeASVtab.R R/makeRankTables.R R/meltData.R R/mergeDatasets.R R/misc.R R/mvEnv.R R/mvhelp.R R/mvload.R R/normalization.R R/orderGroups.R R/parseStratifiers.R R/plotAlphaDiversity.R R/plotBetaDiversity.R R/plotClad.R R/plotDeseq.R R/plotDistributions.R R/plotFeatureCorr.R R/plotGroupedBars.R R/plotHeatTree.R R/plotHeatmap.R R/plotLMEM.R R/plotLefse.R R/plotNetwork.R R/plotPairedCorr.R R/plotRFBoruta.R R/plotRareCurves.R R/plotSimilarity.R R/plotStackedBars.R R/plotUnivar.R R/printmvdata.R R/processMVDataset.R R/rarefyData.R R/resultSaving.R R/sampleFiltering.R R/sampleFrequencies.R R/samplesWith.R R/setFactorVariable.R R/settingSwitches.R R/sparcc.R R/summarizeTaxa.R R/templateFunction.R R/utils-pipe.R R/utils.R README.md man/ASVtoTaxa.Rd man/TaxatoASV.Rd man/activate.Rd man/addGrps.Rd man/addSamples.Rd man/adiv.Rd man/agglomTaxa.Rd man/autonametoggle.Rd man/bdiv.Rd man/calcUniVar.Rd man/capitalize.Rd man/changeFactor.Rd man/changerank.Rd man/checkColors.Rd man/checkFormula.Rd man/checkGroups.Rd man/chooseFactors.Rd man/chooseGrps.Rd man/chooseSamples.Rd man/cleanASVs.Rd man/cleanData.Rd man/cleanGroups.Rd man/cleanUnkTaxa.Rd man/clearFeatureFilt.Rd man/clearNormalization.Rd man/clearProcessing.Rd man/clr.Rd man/clusterSamples.Rd man/colorGrps.Rd man/combineDupeASVs.Rd man/cor2cov.Rd man/countFeatures.Rd man/countSamples.Rd man/countSamples.base.Rd man/excludeFeatures.Rd man/filterLowAbun.Rd man/filterLowPrev.Rd man/filterLowRelAbun.Rd man/filterLowTotAbun.Rd man/filterLowVar.Rd man/filterNAs.Rd man/findSigFisher.Rd man/foldChange.Rd man/ftRatio.Rd man/ftRatiostab.Rd man/ftcor.Rd man/getDiscriminatingFeatures.Rd man/getFeatures.Rd man/getFormulaVars.Rd man/getFtStats.Rd man/getLowestRank.Rd man/getNetwork.Rd man/getParentTaxa.Rd man/getRanks.Rd man/getSamples.Rd man/getdata.Rd man/ggcorrplot.Rd man/glog.Rd man/keepSigFisher.Rd man/listUniques.Rd man/listsigs.Rd man/loadFxnlFile.Rd man/loadMDFile.Rd man/loadTaxaFile.Rd man/makeASVtab.Rd man/makeAldex.Rd man/makeDeseq.Rd man/makePS.Rd man/makeRankTabs.Rd man/makeTaxMap.Rd man/multisave.Rd man/mvCClasso.Rd man/mvLMEM.Rd man/mvNetwork.Rd man/mvaldex.Rd man/mvcombine.Rd man/mvdeseq.Rd man/mvdist.Rd man/mvhelp.Rd man/mvlefse.Rd man/mvload.Rd man/mvmelt.Rd man/mvmerge.Rd man/mvsave.Rd man/mvstratify.Rd man/mvunifrac.Rd man/nameAnalysis.Rd man/nameStratification.Rd man/networkClusters.Rd man/norm_to_total.Rd man/normalizeTable.Rd man/normalizer.Rd man/orderGroups.Rd man/pairedCor.Rd man/parseStratifiers.Rd man/phyloDiversity.Rd man/pipe.Rd man/plotAlphaDiv.Rd man/plotBetaDiv.Rd man/plotClad.Rd man/plotDeseq.Rd man/plotFeatureDensity.Rd man/plotFtCorlines.Rd man/plotFtCormat.Rd man/plotGroupedBars.Rd man/plotHeatTree.Rd man/plotHeatmap.Rd man/plotLEFSE.Rd man/plotLMEM.Rd man/plotNetwork.Rd man/plotPairedCor.Rd man/plotRFImp.Rd man/plotRareCurves.Rd man/plotSampleDensity.Rd man/plotSimilarity.Rd man/plotStackedBars.Rd man/plotUnivar.Rd man/pnova.Rd man/poolGroups.Rd man/posthoctoggle.Rd man/print.mvdata.Rd man/print.mvmerged.Rd man/processDataset.Rd man/pval.sparccboot.Rd man/rangetotext.Rd man/rarefySamples.Rd man/readdepth.Rd man/removeGrps.Rd man/removeLowQuality.Rd man/removePool.Rd man/removeSamples.Rd man/resetResDir.Rd man/rfboruta.Rd man/runFeatureFilter.Rd man/runFeatureRemover.Rd man/runNormalization.Rd man/runRarefaction.Rd man/runSampleFilter.Rd man/sampleFreq.Rd man/samplesWith.Rd man/saveResults.Rd man/savetoggle.Rd man/scaleFeatures.Rd man/scaleSamples.Rd man/selectFeatures.Rd man/setFVar.Rd man/sliceCormats.Rd man/sparcc.Rd man/sparccboot.Rd man/summarizeTaxa.Rd man/theme_mv.Rd man/transData.Rd man/univar.Rd man/unselectFeatures.Rd man/validFactor.Rd man/viewactive.Rd man/viewstats.Rd man/viewtable.Rd man/zeroReplace.Rd man/zerostoggle.Rd tests/testthat.R tests/testthat/test-featureFiltering.R tests/testthat/test-load_taxonomyfile.R