Global functions | |
---|---|
.onLoad | Source code |
KaKsStatistics | Man page Source code |
addAlpha | Man page Source code |
addGeneIdsCols2HomologsKaKsTable | Man page Source code |
addGeneIdsCols2OrthologsKaKsTable | Man page Source code |
alignAAStringSet | Man page Source code |
alignCDSSetWithAlignedAAsAsGuide | Man page Source code |
alignCDSWithAlignedAASeq | Man page Source code |
alignCodingSequencesPipeline | Man page Source code |
alignedForUnalignedAAPos | Man page Source code |
annotationBasedShannonEntropy | Man page Source code |
annotationEvolution | Man page Source code |
annotationMatrix | Man page Source code |
appendToTestedHypotheses | Man page Source code |
axt | Man page Source code |
axtForSelectedDistances | Man page Source code |
buildPhylogeneticTree | Man page Source code |
cbindAnnotationDescription | Man page Source code |
classSpecificExpressionProfileDists | Man page Source code |
closestHomolog | Man page Source code |
codeml.tmpl | Man page |
collectNonConservedAnnotations | Man page Source code |
compositeAnnotations | Man page Source code |
computeKsPipeline | Man page Source code |
computeOrthologSpecificAnnotationDiversityPerGroup | Man page Source code |
computeSpeciesSpecificAnnotationDiversityPerGroup | Man page Source code |
conservedOrthologs | Man page Source code |
constructAnnotationVectorSpace | Man page Source code |
correlationRpkmCopyNo | Man page Source code |
cosAngleVec | Man page Source code |
cosDiag | Man page Source code |
distNormExprVectrs | Man page Source code |
distVectorClouds | Man page Source code |
domainsForPos | Man page Source code |
enrichedAnnotations | Man page Source code |
enrichmentTests | Man page Source code |
euclNorm | Man page Source code |
exprVecSpaceEvolutionAfterDupl | Man page Source code |
expressionProfileDistStatsPerTissues | Man page Source code |
expressionProfilesDists | Man page Source code |
extractFamilyName | Man page Source code |
familyExpanded | Man page Source code |
foregroundNodes | Man page Source code |
formatNodeLabels | Man page Source code |
geneClassesVectorClouds | Man page Source code |
geneGroupSubfunctionalization | Man page Source code |
geneGroupsAnnotationBasedShannonEntropy | Man page Source code |
genePairInRedis | Man page Source code |
generateContingencyTable | Man page Source code |
getFamilyDNAStringSet | Man page Source code |
getMcCores | Man page Source code |
getPairsFromDistForIndices | Man page Source code |
getSpeciesNodeNumberFromCafe | Man page Source code |
getSpliceVariantSeqs | Man page Source code |
goEnrichTest | Man page Source code |
hasInvalidVecSpaceComponents | Man page Source code |
hasInvalidVecSpaceComponents.data.frame | Man page Source code |
hasInvalidVecSpaceComponents.matrix | Man page Source code |
hasInvalidVecSpaceComponents.numeric | Man page Source code |
homologs | Man page Source code |
hyphy.branch.site.bf | Man page |
hyphy.busted.bf | Man page |
hyphy.fubar.bf | Man page |
hyphy.meme.bf | Man page |
inferExpectedFalsePositiveRate | Man page Source code |
interVsIntraSpeciesExpressionProfileDists | Man page Source code |
iprWithSelectedAA | Man page Source code |
joinGOEnrichResults | Man page Source code |
loadDnaFasta | Man page Source code |
matchingSpliceVariant | Man page Source code |
maxMinusMin | Man page Source code |
maxValuesFromInterVsIntraSpeciesExpressionProfileDists | Man page Source code |
mclDataFrameAsList | Man page Source code |
mr.bayes.cds.tree | Man page |
mr.bayes.mixed.cds.tree | Man page |
mr.bayes.mixed.prot.tree | Man page |
mr.bayes.prot.tree | Man page |
mrBayesCdsTree | Man page Source code |
mrBayesProteinTree | Man page Source code |
mrBayesProteinTreeFromMixedMSA | Man page Source code |
mrBayesTreeFromMixedMSA | Man page Source code |
naAsZero | Man page Source code |
nonConservedAnnotations | Man page Source code |
nonConservedCompositeAnnotations | Man page Source code |
normalizeVector | Man page Source code |
numberAnnotations | Man page Source code |
orthologs | Man page Source code |
orthologsFromBLATpslTable | Man page Source code |
parseCafeBranchSpecificPValues | Man page Source code |
parseMemeBranchResults | Man page Source code |
passSupportValues | Man page Source code |
perpVecToDiagonal | Man page Source code |
plotSpeciesSpecificAnnotationDiversity | Man page Source code |
plotSpeciesSpecificAnnotationDiversityDists | Man page Source code |
plotTissueSpecificExpressionProfileDistanceDistribs | Man page Source code |
procGOHyperGResult | Man page Source code |
putGenePairIntoRedis | Man page Source code |
rad2deg | Man page Source code |
readBlatPSLoutput | Man page Source code |
readFubarTable | Man page Source code |
readInterProScanResultTable | Man page Source code |
readKaKsCalculatorOutput | Man page Source code |
readMclOutput | Man page Source code |
readMinimumInterProScanResultTable | Man page Source code |
removeDuplicatedInversePairs | Man page Source code |
removeExpressionVariant | Man page Source code |
removeNodeLabelsAndBranchLengths | Man page Source code |
removeSpliceVariant | Man page Source code |
renderCodemlInputs | Man page Source code |
replaceSanitizedWithOriginalIDs | Man page Source code |
replaceWithOriginal | Man page Source code |
replaceWithOriginalInFigTree | Man page Source code |
sanitizeNames | Man page Source code |
scalarProjection | Man page Source code |
selectGeneGroupSpecificEnrichedAnnotations | Man page Source code |
selectSignificantEnrichments | Man page Source code |
selectSignificantlyEnrichedAnnotations | Man page Source code |
shannonEntropy | Man page Source code |
spec.regex.gene.ids | Man page |
speciesComposition | Man page Source code |
speciesCompositionsToDataFrame | Man page Source code |
speciesForGeneId | Man page Source code |
speciesForGeneId_Regex | Man page Source code |
statVectorCloud | Man page Source code |
subTrees | Man page Source code |
subfunctionalizationAnnotationBased | Man page Source code |
testAlignedForUnalignedAAPos | Man page Source code |
testAnnotationBasedSpeciesSpecificNeofunctionalization | Man page Source code |
testExprVecSpaceEvolutionAfterDupl | Man page Source code |
testGetPairsFromDistForIndices | Man page Source code |
testHomologs | Man page Source code |
testHourglassModel | Man page Source code |
testNonConservedAnnotations | Man page Source code |
testNonConservedCompositeAnnotations | Man page Source code |
testShannonEntropy | Man page Source code |
testSubfunctionalizationAnnotationBased | Man page Source code |
transcriptsPerKilobaseMillion | Man page Source code |
translate2AASeqs | Man page Source code |
tree4Busted | Man page Source code |
unalignedAAforAlignedAAPos | Man page Source code |
upperWhisker | Man page Source code |
validateAASeqs | Man page Source code |
validateAAStringSet | Man page Source code |
vectorProjection | Man page Source code |
writeAxt | Man page Source code |
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