API for asishallab/GeneFamilies
Analyses different properties of gene families

Global functions
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
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
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
getSpeciesNodeNumberFromCafe 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
onLoad Source code
orthologs Man page Source code
orthologsFromBLATpslTable Man page Source code
parseCafeBranchSpecificPValues Man page Source code
parseMemeBranchResults Man page Source code
parseMemeSiteResult 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
testAnnotationBasedSpeciesSpecificNeofunctionalization Man page Source code
testExprVecSpaceEvolutionAfterDupl 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
asishallab/GeneFamilies documentation built on Oct. 5, 2018, 7:26 p.m.