Files in asishallab/GeneFamilies
Analyses different properties of gene families

.gitignore
DESCRIPTION
LICENSE
NAMESPACE
R/annotationVectorSpace.R R/enrichment_funks.R R/expression_funks.R R/family_funks.R R/iprSelectedPositions.R R/ortholog_funks.R R/pairwiseKaKs.R R/phylogenies.R R/plots.R R/selection_funks.R R/utils.R R/zzz.R README.md
data/.gitignore
exec/annotateFamilies.R exec/annotateFamiliesUsingProtDescriptions.R exec/assessDosageEffect.R exec/compareKsDistributionsPerGeneGroups.R exec/computeAnnotationBasedShannonEntropies.R exec/computeExpressionProfileDistances.R exec/computeOrthologsKaKsRatios.R exec/computePairwiseKaKsRatios.R exec/defineGeneSets.R exec/domainBasedFunctionEvolutionAfterDuplication.R exec/domainBasedSubfunctionalizationAfterDuplication.R exec/dosageEffectEnrichedFunctions.R exec/dosageEffectPlots.R exec/expressionAngles.R exec/generateBustedBatchFiles.R exec/generateFubarBatchFiles.R exec/generateNormalizedRpkmExpressionProfiles.R exec/generateRpkmExpressionProfiles.R exec/inferCopyAndTandemNumbers.R exec/investigateDistributionsOfAnnotationBasedShannonEntropies.R exec/investigateDistributionsOfExpressionProfileDistances.R exec/investigateDistributionsOfExpressionProfileDistancesPerTissue.R exec/loadBustedResults.R exec/loadCodingSequences.R exec/loadFubarResults.R exec/loadGeneFamilies.R exec/loadInterProData.R exec/loadMapManAnnotations.R exec/loadOrthologsAndTandems.R exec/loadRpkmRnaSeqCounts.R exec/mapManRootBinAnnotations.R exec/parseCafeResult.R exec/plotDistributionsOfExpressionProfileDistances.R exec/plotDistributionsOfExpressionProfileDistancesPerTissue.R exec/plotDomainArchitectureDiversitiesPerMapManGroup.R exec/plotExpressionDiversitiesPerMapManGroup.R exec/reconstructFamilyPhylogenies.R
inst/macse_v1.01b.jar
inst/mcl2orthoformat.pl
man/addAlpha.Rd man/addGeneIdsCols2HomologsKaKsTable.Rd man/addGeneIdsCols2OrthologsKaKsTable.Rd man/alignAAStringSet.Rd man/alignCDSSetWithAlignedAAsAsGuide.Rd man/alignCDSWithAlignedAASeq.Rd man/alignCodingSequencesPipeline.Rd man/annotationBasedShannonEntropy.Rd man/annotationEvolution.Rd man/annotationMatrix.Rd man/appendToTestedHypotheses.Rd man/axt.Rd man/buildPhylogeneticTree.Rd man/cbindAnnotationDescription.Rd man/classSpecificExpressionProfileDists.Rd man/closestHomolog.Rd man/codeml.tmpl.Rd man/collectNonConservedAnnotations.Rd man/compositeAnnotations.Rd man/computeKsPipeline.Rd man/computeOrthologSpecificAnnotationDiversityPerGroup.Rd man/computeSpeciesSpecificAnnotationDiversityPerGroup.Rd man/conservedOrthologs.Rd man/constructAnnotationVectorSpace.Rd man/correlationRpkmCopyNo.Rd man/cosAngleVec.Rd man/cosDiag.Rd man/distNormExprVectrs.Rd man/distVectorClouds.Rd man/domainsForPos.Rd man/enrichedAnnotations.Rd man/enrichmentTests.Rd man/euclNorm.Rd man/exprVecSpaceEvolutionAfterDupl.Rd man/expressionProfileDistStatsPerTissues.Rd man/expressionProfilesDists.Rd man/extractFamilyName.Rd man/familyExpanded.Rd man/foregroundNodes.Rd man/formatNodeLabels.Rd man/geneClassesVectorClouds.Rd man/geneGroupSubfunctionalization.Rd man/geneGroupsAnnotationBasedShannonEntropy.Rd man/genePairInRedis.Rd man/generateContingencyTable.Rd man/getFamilyDNAStringSet.Rd man/getMcCores.Rd man/getSpeciesNodeNumberFromCafe.Rd man/goEnrichTest.Rd man/hasInvalidVecSpaceComponents.Rd man/hasInvalidVecSpaceComponents.data.frame.Rd man/hasInvalidVecSpaceComponents.matrix.Rd man/hasInvalidVecSpaceComponents.numeric.Rd man/homologs.Rd man/hyphy.branch.site.bf.Rd man/hyphy.busted.bf.Rd man/hyphy.fubar.bf.Rd man/hyphy.meme.bf.Rd man/inferExpectedFalsePositiveRate.Rd man/interVsIntraSpeciesExpressionProfileDists.Rd man/iprWithSelectedAA.Rd man/joinGOEnrichResults.Rd man/loadDnaFasta.Rd man/matchingSpliceVariant.Rd man/maxMinusMin.Rd man/maxValuesFromInterVsIntraSpeciesExpressionProfileDists.Rd man/mclDataFrameAsList.Rd man/mr.bayes.cds.tree.Rd man/mr.bayes.mixed.cds.tree.Rd man/mr.bayes.mixed.prot.tree.Rd man/mr.bayes.prot.tree.Rd man/mrBayesCdsTree.Rd man/mrBayesProteinTree.Rd man/mrBayesProteinTreeFromMixedMSA.Rd man/mrBayesTreeFromMixedMSA.Rd man/naAsZero.Rd man/nonConservedAnnotations.Rd man/nonConservedCompositeAnnotations.Rd man/normalizeVector.Rd man/numberAnnotations.Rd man/orthologs.Rd man/orthologsFromBLATpslTable.Rd man/parseCafeBranchSpecificPValues.Rd man/parseMemeBranchResults.Rd man/passSupportValues.Rd man/perpVecToDiagonal.Rd man/plotSpeciesSpecificAnnotationDiversity.Rd man/plotSpeciesSpecificAnnotationDiversityDists.Rd man/plotTissueSpecificExpressionProfileDistanceDistribs.Rd man/procGOHyperGResult.Rd man/putGenePairIntoRedis.Rd man/rad2deg.Rd man/readBlatPSLoutput.Rd man/readFubarTable.Rd man/readInterProScanResultTable.Rd man/readKaKsCalculatorOutput.Rd man/readMclOutput.Rd man/readMinimumInterProScanResultTable.Rd man/removeDuplicatedInversePairs.Rd man/removeExpressionVariant.Rd man/removeNodeLabelsAndBranchLengths.Rd man/removeSpliceVariant.Rd man/renderCodemlInputs.Rd man/replaceSanitizedWithOriginalIDs.Rd man/replaceWithOriginal.Rd man/replaceWithOriginalInFigTree.Rd man/sanitizeNames.Rd man/scalarProjection.Rd man/selectGeneGroupSpecificEnrichedAnnotations.Rd man/selectSignificantEnrichments.Rd man/selectSignificantlyEnrichedAnnotations.Rd man/shannonEntropy.Rd man/spec.regex.gene.ids.Rd man/speciesComposition.Rd man/speciesCompositionsToDataFrame.Rd man/speciesForGeneId.Rd man/speciesForGeneId_Regex.Rd man/statVectorCloud.Rd man/subTrees.Rd man/subfunctionalizationAnnotationBased.Rd man/testAnnotationBasedSpeciesSpecificNeofunctionalization.Rd man/testExprVecSpaceEvolutionAfterDupl.Rd man/testHomologs.Rd man/testHourglassModel.Rd man/testNonConservedAnnotations.Rd man/testNonConservedCompositeAnnotations.Rd man/testShannonEntropy.Rd man/testSubfunctionalizationAnnotationBased.Rd man/transcriptsPerKilobaseMillion.Rd man/translate2AASeqs.Rd man/tree4Busted.Rd man/unalignedAAforAlignedAAPos.Rd man/upperWhisker.Rd man/validateAASeqs.Rd man/validateAAStringSet.Rd man/vectorProjection.Rd man/writeAxt.Rd
tags
vignettes/GeneFamilies.Rmd
vignettes/GeneFamilies.html
asishallab/GeneFamilies documentation built on Oct. 5, 2018, 7:26 p.m.