API for HCBravoLab/metagenomeSeq
Statistical analysis for sparse high-throughput sequencing
| Global functions | |
|---|---|
| .do_fitZig | Source code |
| MRcoefs | Man page Source code |
| MRcounts | Man page Source code |
| MRcounts,MRexperiment-method | Man page |
| MRexperiment-class | Man page |
| MRexperiment2biom | Man page Source code |
| MRfulltable | Man page Source code |
| MRihw | Man page |
| MRihw,fitFeatureModelResults-method | Man page |
| MRihw,fitZigResults-method | Man page |
| MRtable | Man page Source code |
| [,MRexperiment,ANY,ANY,ANY-method | Man page |
| [,MRexperiment-method | Man page |
| aggSamp | Man page Source code |
| aggTax | Man page Source code |
| aggregateBySample | Man page Source code |
| aggregateByTaxonomy | Man page Source code |
| biom2MRexperiment | Man page Source code |
| calcNormFactors | Man page Source code |
| calcPosComponent | Man page Source code |
| calcShrinkParameters | Man page Source code |
| calcStandardError | Man page Source code |
| calcZeroAdjustment | Man page Source code |
| calcZeroComponent | Man page Source code |
| calculateEffectiveSamples | Man page Source code |
| colMeans,MRexperiment-method | Man page |
| colSums,MRexperiment-method | Man page |
| corTest | Man page |
| correctIndices | Man page Source code |
| correlationTest | Man page Source code |
| cumNorm | Man page Source code |
| cumNormMat | Man page Source code |
| cumNormStat | Man page Source code |
| cumNormStatFast | Man page Source code |
| deprecated_metagenomeSeq_function | Man page Source code |
| doCountMStep | Man page Source code |
| doEStep | Man page Source code |
| doZeroMStep | Man page Source code |
| expSummary | Man page Source code |
| expSummary,MRexperiment-method | Man page |
| exportMat | Man page Source code |
| exportMatrix | Man page |
| exportStats | Man page Source code |
| extractMR | Man page Source code |
| filterData | Man page Source code |
| fitDO | Man page Source code |
| fitFeatureModel | Man page Source code |
| fitFeatureModelResults-class | Man page |
| fitLogNormal | Man page Source code |
| fitMeta | Man page Source code |
| fitMultipleTimeSeries | Man page Source code |
| fitPA | Man page Source code |
| fitSSTimeSeries | Man page Source code |
| fitTimeSeries | Man page Source code |
| fitZeroLogNormal | Man page Source code |
| fitZig | Man page Source code |
| fitZigResults-class | Man page |
| genusPlot | Man page |
| getCountDensity | Man page Source code |
| getEpsilon | Man page Source code |
| getNegativeLogLikelihoods | Man page Source code |
| getPi | Man page Source code |
| getZ | Man page Source code |
| isItStillActive | Man page Source code |
| libSize | Man page |
| libSize,MRexperiment-method | Man page |
| libSize<- | Man page |
| libSize<-,MRexperiment,numeric-method | Man page |
| loadBiom | Man page Source code |
| loadMeta | Man page Source code |
| loadMetaQ | Man page Source code |
| loadPhenoData | Man page Source code |
| load_biom | Man page Source code |
| load_meta | Man page Source code |
| load_metaQ | Man page Source code |
| load_phenoData | Man page Source code |
| lungData | Man page |
| makeLabels | Man page Source code |
| mergeMRexperiments | Man page Source code |
| mergeTable | Man page Source code |
| metadata | Source code |
| metagenomeSeq | Man page |
| metagenomeSeq-deprecated | Man page |
| metagenomeSeq-package | Man page |
| metagenomicLoader | Man page |
| mouseData | Man page |
| newMRexperiment | Man page Source code |
| normFactors | Man page |
| normFactors,MRexperiment-method | Man page |
| normFactors<- | Man page |
| normFactors<-,MRexperiment,numeric-method | Man page |
| phenoData | Man page |
| plotBubble | Man page Source code |
| plotClassTimeSeries | Man page Source code |
| plotCorr | Man page Source code |
| plotFeature | Man page Source code |
| plotGenus | Man page Source code |
| plotMRheatmap | Man page Source code |
| plotOTU | Man page Source code |
| plotOrd | Man page Source code |
| plotRare | Man page Source code |
| plotTimeSeries | Man page Source code |
| posteriorProbs | Man page Source code |
| posteriorProbs,MRexperiment-method | Man page |
| qiimeLoader | Man page |
| returnAppropriateObj | Man page Source code |
| rowMeans,MRexperiment-method | Man page |
| rowSums,MRexperiment-method | Man page |
| settings2 | Man page |
| ssFit | Man page Source code |
| ssIntervalCandidate | Man page Source code |
| ssPerm | Man page Source code |
| ssPermAnalysis | Man page Source code |
| trapz | Man page Source code |
| ts2MRexperiment | Man page Source code |
| uniqueFeatures | Man page Source code |
| wrenchNorm | Man page Source code |
| zigControl | Man page Source code |
