Man pages for YTLogos/myTAI
Evolutionary Transcriptomics

age.applyAge Category Specific apply Function
bar.colorsColor palette for barplots
bootMatrixCompute a Permutation Matrix for Test Statistics
CollapseReplicatesCombine Replicates in an ExpressionSet
combinatorialSignificanceCompute the Statistical Significance of Each Replicate...
DiffGenesDifferential Gene Expression Analysis
DivergenceExpressionSetExampleAn Example DivergenceExpressionSet Data Set
EarlyConservationTestPerform Reductive Early Conservation Test
ecScoreCompute the Hourglass Score for the EarlyConservationTest
EnrichmentTestPhylostratum or Divergence Stratum Enrichment of a given Gene...
ExpressedFilter for Expressed Genes
FlatLineTestPerform Flat Line Test
geom.meanGeometric Mean
GroupDiffsQuantify the significant differences between gene expression...
harm.meanHarmonic Mean
is.ExpressionSetTest ExpressionSet Standard
MatchMapMatch a Phylostratigraphic Map or Divergence Map with a...
omitMatrixCompute TAI or TDI Profiles Omitting a Given Gene
PhyloExpressionSetExampleAn Example PhyloExpressionSet Data Set
PlotBarREPlot Mean Relative Expression Levels as Barplot
PlotCategoryExprPlot the Expression Levels of each Age or Divergence Category...
PlotCIRatioPlot Transcriptome Index using bootstrapping and confidence...
PlotContributionPlot Cumuative Transcriptome Index
PlotCorrelationPlot the Correlation Between Phylostrata and Divergence...
PlotDistributionPlot the Frequency Distribution of Phylostrata or Divergence...
PlotEnrichmentPlot the Phylostratum or Divergence Stratum Enrichment of a...
PlotGeneSetPlot the Expression Profiles of a Gene Set
PlotGroupDiffsPlot the significant differences between gene expression...
PlotMeansPlot Mean Expression Profiles
PlotMediansPlot Median Expression Profiles
PlotPatternPlot the Transcriptome Age Index or Transcriptome Divergence...
PlotREPlot Relative Expression Levels
PlotReplicateQualityPlot the Quality of Biological Replicates
PlotSelectedAgeDistrPlot the PS or DS distribution of a selected set of genes
PlotSignaturePlot evolutionary signatures across transcriptomes
PlotVarsPlot Variance of Expression Profiles
pMatrixCompute Partial TAI or TDI Values
pStrataCompute Partial Strata Values
pTAICompute the Phylostratum Contribution to the Global...
pTDICompute the Divergence Stratum Contribution to the Global...
RETransform to Relative Expression Levels
ReductiveHourglassTestPerform the Reductive Hourglass Test
REMatrixCompute a Relative Expression Matrix
rhScoreCompute the Hourglass Score for the Reductive Hourglass Test
SelectGeneSetSelect a Subset of Genes in an ExpressionSet
TAICompute the Transcriptome Age Index (TAI)
taxidRetrieve taxonomy categories from NCBI Taxonomy
taxonomyRetrieving Taxonomic Information of a Query Organism
TDICompute the Transcriptome Divergence Index (TDI)
tfTransform Gene Expression Levels
TPICompute the Transcriptome Polymorphism Index (TPI)
YTLogos/myTAI documentation built on Jan. 1, 2018, 12:29 a.m.