API for walterxie/ComMA
Community Matrix Analysis

Global functions
CMStatistics Man page
ComMA Man page
ComMA-package Man page
CommunityComparison Man page
CommunityPhyloStru Man page
EUtils Man page
IOComMA Man page
JostDiversity Man page
PlotPrioritisation Man page
RDA Man page
ReadsOTUsTaxa Man page
TaxaUtils Man page
TreeUtils Man page
TurnoverDist Man page Source code
UtilsCombine Man page
abundancePerSample Man page Source code
annotateRAXMLTree Man page Source code
assignTaxaByRank Man page Source code
batchDownload Man page Source code
beta1minus1 Man page Source code
checkLabel2 Source code
classification Man page
combineTaxaAssign Man page Source code
combineTriMatrix Man page Source code
combineTwoDF Man page Source code
convertType Man page Source code
corrEnterotypeToGroup Man page Source code
countCharOccurrences Man page Source code
createTaxaTableMEGAN Man page Source code
createTaxaTableRDP Man page Source code
ctreeClassification Man page Source code
deg2rad Man page Source code
dist.JSD Source code
distance Man page
diverrare Man page
diversityTable Man page Source code
doRDA Man page Source code
enterotype Man page
enterotypePipeline Man page Source code
findDuplicates Man page Source code
firstN Man page Source code
freqUniqueValue Man page Source code
gcd Man page Source code
gcd.hf Man page Source code
gcd.slc Man page Source code
gcd.vif Man page Source code
geodesicDist.hf Man page Source code
geodesicDist.slc Man page Source code
getClusters Man page Source code
getCombPlotPrior.JostDiver Source code
getCountsSums Man page Source code
getDataCluster Man page Source code
getDissimilarity Man page Source code
getDissimilarityList Man page Source code
getDiverRare Man page Source code
getFirstNInString Man page Source code
getJSD Man page Source code
getLabelMatchedDist Source code
getMethodLines Man page Source code
getMultiDiverRare Man page Source code
getPhylorareDF Man page Source code
getPlotPrior Man page Source code
getPlotPrior.JostDiver Man page Source code
getPlotPrior.JostDiver2 Source code
getPlotPrior.PhyloAlpha Man page Source code
getPlural Man page Source code
getRanks Source code
getRelativeAbundance Man page Source code
getSubsamplesForDiverRare Man page Source code
getTaxaAssg Source code
getTaxaAssg2 Source code
getTaxaMap Man page Source code
getTriMatrix Man page Source code
ggDiverRare Man page Source code
groupsTaxaMembers Man page Source code
gsubDF Man page Source code
installAllPackages Man page Source code
lassoClassification Man page Source code
mantelComparison Man page Source code
matchCMEnv Man page Source code
mergeBy Man page Source code
mergeCMTaxa Man page Source code
mergeListOfDF Man page Source code
mergePlotPriorListOfDF Man page Source code
mkDir Man page Source code
mkValidTex Source code
mostAbundantRows Man page Source code
mvRowsToLast Man page Source code
nmdsTriMatrix Man page Source code
noise.removal Man page Source code
normalize Man page Source code
orderDiversityDF Source code
pam.clustering Source code
parseTSeqSet Man page Source code
parseTaxaSet Man page Source code
pasteDF Man page Source code
phylo.alpha Man page Source code
phylo.beta.dist Man page Source code
phylo.mntd Man page Source code
phylo.mpd Man page Source code
phylo.unifrac.dist Man page Source code
phylorare Source code
plotCascadeKM Source code
plotClusterAbundence Man page Source code
plotCombinedTriMatrix Man page Source code
plotCorrelations Man page Source code
plotEnterotypes Man page Source code
plotEnterotypes.bak Source code
plotOptClusters Man page Source code
plotPDBeta Man page Source code
plotPrioritisation Man page Source code
plotPrioritisation.NeatMap Man page Source code
plotPrioritisation.Phyloseq Man page Source code
plotProcrustes Man page Source code
plotRDA Man page Source code
plotSamples Source code
plotTaxonomy Man page Source code
prepTaxonomy Man page Source code
preprocessCM Man page Source code
preprocessEnv Man page Source code
prettyNumbers Man page Source code
printResult Man page Source code
printXTable Man page Source code
printXTable.RDA Man page Source code
procrustesComparison Man page Source code
readCodeCoverage Man page Source code
readCommunityMatrix Man page Source code
readFile Man page Source code
readFileLineByLine Man page Source code
readMCMCLog Man page Source code
readTaxaTable Man page Source code
renameFastaID Man page Source code
renameTips Man page Source code
richnessPerSample Man page Source code
rmDuplicateSeq Man page Source code
rmMinAbundance Man page Source code
seqSet2Fasta Man page Source code
shannonPerSample Man page Source code
simpleCap Man page Source code
spatial Man page
spilt.df Man page Source code
splitPath Man page Source code
stringUtils Man page
sublistByPairs Man page Source code
subsetCM Man page Source code
subsetSequences Man page Source code
subsetTaxaTable Man page Source code
substrBetween Man page Source code
substrLast Man page Source code
substrLastSplit Man page Source code
sumColumns Man page Source code
summReadsOTUsPipeline Man page Source code
summaryCM Man page Source code
summaryCM.Vector Man page Source code
summaryCMPerSample Man page Source code
summaryDiversity Man page Source code
summaryOTUs Man page Source code
summaryRank Man page Source code
summaryTaxaAssign Man page Source code
summaryTaxaGroup Man page Source code
taxonomyAssignment Source code
taxonomyAssignment2 Source code
transposeDF Man page Source code
trimSpace Man page Source code
trimSpace.old Source code
trimStartEndSpace Man page Source code
unwrapInputList Source code
utilsCM Man page
utilsSeq Man page
validateCluster Source code
vif_func Source code
writeCommunityMatrix Man page Source code
writeTable Man page Source code
walterxie/ComMA documentation built on July 1, 2017, 2:03 a.m.