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/analizeLightExpression.R
exec/analizeLightExpressionFoldChange.R
exec/annotateFamilies.R
exec/annotateFamiliesUsingProtDescriptions.R
exec/assessDosageEffect.R
exec/calculateDuplicationKsStats.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/measure_PSII_to_PSI_ratios.R
exec/parseCafeResult.R
exec/plotDistributionsOfExpressionProfileDistances.R
exec/plotDistributionsOfExpressionProfileDistancesPerTissue.R
exec/plotDomainArchitectureDiversitiesPerMapManGroup.R
exec/plotExpressionDiversitiesPerMapManGroup.R
exec/plotGeneGroupSizes.R
exec/reconstructFamilyPhylogenies.R
inst/1_UP_in_Ch_only.txt
inst/2_UP_in_At_only.txt
inst/3_DOWN_in_Ch_only.txt
inst/4_DOWN_in_At_only.txt
inst/5_UP_in_Ch+At_shared.txt
inst/6_DOWN_in_Ch+At_shared.txt
inst/DuplicatedKsStats.pdf
inst/ExpressedGeneGroupsVenn.pdf
inst/GeneFunctionEvolution.pdf
inst/GeneGroupsVenn.pdf
inst/KaKs_Calculator
inst/MAPP.jar
inst/PS_II_over_PS_I_ratios.txt
inst/RNA_Seq_RPKM_and_profiles.tsv
inst/absLog2FoldChangeIntraSpeciesBoxplots.pdf
inst/absoluteFunctionDiversitiesInterGeneGroupClasses_h-tests.tsv
inst/absoluteFunctionDiversitiesPerGeneGroupClassesAndOrthologDistinctionBoxplot.pdf
inst/absoluteFunctionDiversitiesPerGeneGroupClassesAndOrthologDistinctionBoxplot_NoPosSel.pdf
inst/absoluteFunctionDiversitiesPerGeneGroupClassesBoxplot.pdf
inst/absoluteFunctionDiversitiesPerGeneGroupClassesBoxplot_NoPosSel.pdf
inst/absoluteFunctionDiversitiesPerGeneGroupClasses_h-tests.tsv
inst/afterDuplicationAngleBetweenOrth2DiagVecsBoxplot.pdf
inst/afterDuplicationAngleBetweenOrth2DiagVecsHistograms.pdf
inst/ath.light.allgenes.txt
inst/chi.light.allgenes.txt
inst/copyNoRpkmLog2Scatter.pdf
inst/copyNoRpkmScatter.pdf
inst/domainArchitectureDiversityPerMapManRootBinFamiliesBoxplots.pdf
inst/domainArchitectureDiversityPerMapManRootBinTandemsBoxplots.pdf
inst/expandedFamsTissueSpecificExpressionProfileDistancesBoxplot.pdf
inst/expressionAngleToDiagonalBoxplot.pdf
inst/expressionDiversityPerMapManRootBinFamiliesBoxplots.pdf
inst/expressionDiversityPerMapManRootBinTandemsBoxplots.pdf
inst/geneFamilyAndTandemClusterSizesBoxplot.pdf
inst/gsea-3.0.jar
inst/hourglassModel_T_Tests_expandedFamilies.tsv
inst/hourglassModel_T_Tests_positivelySelectedFamilies.tsv
inst/hourglassModel_T_Tests_tandems.tsv
inst/jaume_light_genes_de.txt
inst/light_ath_chi_fisher_tests_sign_mapManBins.txt
inst/light_ath_chi_fisher_tests_sign_mapManBins_genes.txt
inst/light_ath_fisher_tests_sign_mapManBins.txt
inst/light_ath_fisher_tests_sign_mapManBins_genes.txt
inst/light_chi_fisher_tests_sign_mapManBins.txt
inst/light_chi_fisher_tests_sign_mapManBins_genes.txt
inst/light_expression_ath_chi.rnk
inst/light_genes_de_foldChange_ath_chi_down_overrep_MapManBins.txt
inst/light_genes_de_foldChange_ath_chi_up_overrep_MapManBins.txt
inst/light_genes_de_foldChange_ath_down_overrep_MapManBins.txt
inst/light_genes_de_foldChange_ath_up_overrep_MapManBins.txt
inst/light_genes_de_foldChange_chi_down_overrep_MapManBins.txt
inst/light_genes_de_foldChange_chi_up_overrep_MapManBins.txt
inst/macse_v1.01b.jar
inst/mapManBins.gmt
inst/mcl2orthoformat.pl
inst/meanChangeInAngleBetweenOrthOnDiagsBoxplot.pdf
inst/meanTissueVersatilityDiffsAfterDuplicationBoxplot.pdf
inst/meanTissueVersatilityDiffsAfterDuplicationHistograms.pdf
inst/medianExpressionDistsTandemNonOrthsAndExpandedNonOrthsHist.pdf
inst/medianExpressionProfileDistancesPerGeneGroupClassesAndOrthologDistinctionBoxplot.pdf
inst/medianExpressionProfileDistancesPerGeneGroupClassesAndOrthologDistinctionBoxplot_NoPosSel.pdf
inst/medianExpressionProfileDistancesPerGeneGroupClassesAndOrthologDistinctionBoxplot_h-tests.txt
inst/medianExpressionProfileDistancesPerGeneGroupClassesBoxplot.pdf
inst/medianExpressionProfileDistancesPerGeneGroupClassesBoxplot_NoPosSel.pdf
inst/medianExpressionProfileDistancesPerGeneGroupClassesBoxplot_h-tests.txt
inst/normalizedFunctionDiversitiesInterGeneGroupClasses_h-tests.tsv
inst/normalizedFunctionDiversitiesPerGeneGroupClassesAndOrthologDistinctionBoxplot.pdf
inst/normalizedFunctionDiversitiesPerGeneGroupClassesAndOrthologDistinctionBoxplot_NoPosSel.pdf
inst/normalizedFunctionDiversitiesPerGeneGroupClassesBoxplot.pdf
inst/normalizedFunctionDiversitiesPerGeneGroupClassesBoxplot_NoPosSel.pdf
inst/normalizedFunctionDiversitiesPerGeneGroupClasses_h-tests.tsv
inst/pairwiseKaKs.tsv
inst/posSelFamsTissueSpecificExpressionProfileDistancesBoxplot.pdf
inst/relativeExpressionVersatilityBoxplot.pdf
inst/rpkmNormalizdExpressionProfilesExpTandsScatter.pdf
inst/spe8_ortho_concate_ml_gamma_rescaled_ultrametric.newick
inst/tandNoRpkmLog2Scatter.pdf
inst/tandNoRpkmScatter.pdf
inst/tandemsTissueSpecificExpressionProfileDistancesBoxplot.pdf
man/KaKsStatistics.Rd
man/addAlpha.Rd
man/addGeneIdsCols2HomologsKaKsTable.Rd
man/addGeneIdsCols2OrthologsKaKsTable.Rd
man/alignAAStringSet.Rd
man/alignCDSSetWithAlignedAAsAsGuide.Rd
man/alignCDSWithAlignedAASeq.Rd
man/alignCodingSequencesPipeline.Rd
man/alignedForUnalignedAAPos.Rd
man/annotationBasedShannonEntropy.Rd
man/annotationEvolution.Rd
man/annotationMatrix.Rd
man/appendToTestedHypotheses.Rd
man/axt.Rd
man/axtForSelectedDistances.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/getPairsFromDistForIndices.Rd
man/getSpeciesNodeNumberFromCafe.Rd
man/getSpliceVariantSeqs.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/testAlignedForUnalignedAAPos.Rd
man/testAnnotationBasedSpeciesSpecificNeofunctionalization.Rd
man/testExprVecSpaceEvolutionAfterDupl.Rd
man/testGetPairsFromDistForIndices.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/EasyVectorOmics.Rmd
vignettes/GeneFamilies.Rmd
vignettes/GeneFamilies.html
