| .onLoad |
Source code
|
| PhyloFun |
Man page
|
| PhyloFun-package |
Man page
|
| ancestorGoTermsForAccession |
Source code
|
| ancestralGoTerms |
Source code
|
| bestHits |
Source code
|
| buildVectorSpaceModel |
Source code
|
| chooseFilteredAlignment |
Source code
|
| commandLineArguments |
Source code
|
| conditionalProbabilityTable |
Source code
|
| conditionalProbabilityTables |
Source code
|
| connectToGeneOntology |
Source code
|
| constructVectorSpaceModel |
Source code
|
| cumulativeBranchLengthsToRoot |
Source code
|
| distanceIndices |
Source code
|
| distanceMatrixIndices |
Source code
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| domainArchitectureDistances |
Source code
|
| domainSpaceVectors |
Source code
|
| downloadSequences |
Source code
|
| downloadUniprotDocuments |
Source code
|
| edge.to.formula |
Source code
|
| edgeIndex |
Source code
|
| extendGOAnnosWithParents |
Source code
|
| extractAnnotations |
Source code
|
| extractExperimentallyVerifiedGoAnnos |
Source code
|
| extractName |
Source code
|
| extractRefSeqAccession |
Source code
|
| extractUniprotAccessionFromUniprotName |
Source code
|
| fScore |
Source code
|
| fScores |
Source code
|
| falsePositiveRates |
Source code
|
| falsePositives |
Source code
|
| falsePositivesUpperBound |
Source code
|
| filterAnnotationMutationProbabilityTableList |
Source code
|
| filterMultipleSequenceAlignment |
Source code
|
| findMatchingRow |
Source code
|
| generateDomainArchitectureSpaceVectorRedis |
Source code
|
| generateDomainArchitectureSpaceVectors |
Source code
|
| get.node.label |
Source code
|
| get.root.node |
Source code
|
| getDescendantNodes |
Source code
|
| getEntries |
Source code
|
| getEvidenceCode |
Source code
|
| goAnnotationAbbreviations |
Source code
|
| goAnnotationSpaceAbbreviations |
Source code
|
| goProfile |
Source code
|
| goTermForAccession |
Source code
|
| goTermForAccessionOrSynonym |
Source code
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| goTermsForAccession |
Source code
|
| goTermsForAccessionOrSynonymWithLevel |
Source code
|
| goTermsForAccessionWithDefinition |
Source code
|
| goTermsForAccessionWithDefinitionAndLevel |
Source code
|
| goTermsForAccessionWithLevel |
Source code
|
| goTermsForProteinAccession |
Source code
|
| goTermsForProteinAccessionsAndEvidenceCodes |
Source code
|
| goTermsOfLevelAndType |
Source code
|
| gridPMutation |
Source code
|
| homologsStats |
Source code
|
| htmlReport |
Source code
|
| initializeDomainAnnotations |
Source code
|
| initializeDomainWeights |
Source code
|
| intersectAnnotations |
Source code
|
| join.funk |
Source code
|
| joinGOTermMutationProbabilityTables |
Source code
|
| maxDistanceToRoot |
Source code
|
| measureEuclideanDists |
Source code
|
| mergeQueryPredictionsAndHomologAnnotations |
Source code
|
| msaEqual |
Source code
|
| msaStats |
Source code
|
| mutationProbability |
Source code
|
| mutationProbabilityDistribution |
Source code
|
| pMutation |
Source code
|
| pMutationMinMaxParentValues |
Source code
|
| pairsForAccessions |
Source code
|
| pairsForAccessionsAssumingSymmetry |
Source code
|
| pairsFromBlastResult |
Source code
|
| pairwiseDistanceKey |
Source code
|
| pairwiseDomainArchitectureDistance |
Source code
|
| pairwiseDomainArchitectureDistanceRedis |
Source code
|
| pairwiseSequenceDistance |
Source code
|
| pairwiseSequenceDistanceRedis |
Source code
|
| pairwiseVectorSpaceModel |
Source code
|
| parentChildRelation |
Source code
|
| parentGoTerms |
Source code
|
| parentGoTermsForAccession |
Source code
|
| parentGoTermsOfLevel |
Source code
|
| parentGoTermsOfLevelForAccessions |
Source code
|
| parentNode |
Source code
|
| parseBlast2GOresults |
Source code
|
| parseBlastTable |
Source code
|
| parseInterProScan2GOresults |
Source code
|
| parseInterProScanTable |
Source code
|
| parsePhmmerTable |
Source code
|
| partialDomainArchitectureDistances |
Source code
|
| partialDomainArchitectureDistancesRedis |
Source code
|
| partialSequenceDistances |
Source code
|
| partialSequenceDistancesRedis |
Source code
|
| plotPhyloFunTree |
Source code
|
| preProcessHmmerTable |
Source code
|
| precision |
Source code
|
| project.file.path |
Source code
|
| proteinPairsSharingAnnotation |
Source code
|
| rates |
Source code
|
| rcpp_hello_world |
Man page
|
| recall |
Source code
|
| recallRates |
Source code
|
| replaceSelenocystein |
Source code
|
| replaceSelenocysteinInFasta |
Source code
|
| retrieveAnnotations |
Source code
|
| retrieveAnnotationsBiomart |
Source code
|
| retrieveExperimentallyVerifiedGOAnnotations |
Source code
|
| retrieveGOAnnotations |
Source code
|
| retrieveUniprotAnnotations |
Source code
|
| roundBranchLengths |
Source code
|
| sanitizeUniprotAccession |
Source code
|
| sanitizeUniprotAccessions |
Source code
|
| selectMostSignificantEvidenceCode |
Source code
|
| sequenceDistances |
Source code
|
| sharedAnnotation |
Source code
|
| sortedPairName |
Source code
|
| spawnedGoTerms |
Source code
|
| specificity |
Source code
|
| specificityRates |
Source code
|
| truePositivesUpperBound |
Source code
|
| truesUpperBound |
Source code
|
| uniprotkb.url |
Source code
|
| uniq.annotations |
Source code
|
| uniqueGOAnnotationsWithMostSignificantEvidenceCodes |
Source code
|
| uniqueHomologs |
Source code
|
| uniquePairs |
Source code
|
| uniqueProteinPairs |
Source code
|
