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CollapseReplicates()
|
Combine Replicates in an ExpressionSet |
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CombinatorialSignificance()
|
Compute the Statistical Significance of Each Replicate Combination |
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DiffGenes()
|
Differential Gene Expression Analysis |
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DivergenceExpressionSetExample
|
An Example DivergenceExpressionSet Data Set |
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EarlyConservationTest()
|
Perform Reductive Early Conservation Test |
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EnrichmentTest()
|
Phylostratum or Divergence Stratum Enrichment of a given Gene Set based on Fisher's Test |
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Expressed()
|
Filter for Expressed Genes |
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FlatLineTest()
|
Perform Flat Line Test |
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GroupDiffs()
|
Quantify the significant differences between gene expression distributions of age groups |
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MatchMap()
|
Match a Phylostratigraphic Map or Divergence Map with a ExpressionMatrix |
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PhyloExpressionSetExample
|
An Example PhyloExpressionSet Data Set |
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PlotBarRE()
|
Plot Mean Relative Expression Levels as Barplot |
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PlotCIRatio()
|
Plot Transcriptome Index using bootstrapping and confidence intervals |
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PlotCategoryExpr()
|
Plot the Expression Levels of each Age or Divergence Category as Boxplot, Violinplot, or Dotplot |
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PlotContribution()
|
Plot Cumuative Transcriptome Index |
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PlotCorrelation()
|
Plot the Correlation Between Phylostrata and Divergence Strata |
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PlotDistribution()
|
Plot the Frequency Distribution of Phylostrata or Divergence Strata |
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PlotEnrichment()
|
Plot the Phylostratum or Divergence Stratum Enrichment of a given Gene Set |
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PlotGeneSet()
|
Plot the Expression Profiles of a Gene Set |
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PlotGroupDiffs()
|
Plot the significant differences between gene expression distributions of PS or DS groups |
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PlotMeans()
|
Plot Mean Expression Profiles |
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PlotMedians()
|
Plot Median Expression Profiles |
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PlotPattern()
|
Plot the Transcriptome Age Index or Transcriptome Divergence Index |
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PlotRE()
|
Plot Relative Expression Levels |
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PlotReplicateQuality()
|
Plot the Quality of Biological Replicates |
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PlotSelectedAgeDistr()
|
Plot the PS or DS distribution of a selected set of genes |
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PlotSignature()
|
Plot evolutionary signatures across transcriptomes |
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PlotVars()
|
Plot Variance of Expression Profiles |
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RE()
|
Transform to Relative Expression Levels |
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REMatrix()
|
Compute a Relative Expression Matrix |
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ReductiveHourglassTest()
|
Perform the Reductive Hourglass Test |
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ReverseHourglassTest()
|
Perform the Reverse Hourglass Test |
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SelectGeneSet()
|
Select a Subset of Genes in an ExpressionSet |
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TAI()
|
Compute the Transcriptome Age Index (TAI) |
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TDI()
|
Compute the Transcriptome Divergence Index (TDI) |
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TEI()
|
Compute the Transcriptome Evolutionary Index (TEI) |
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TPI()
|
Compute the Transcriptome Polymorphism Index (TPI) |
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age.apply()
|
Age Category Specific apply Function |
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bar.colors()
|
Color palette for barplots |
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bootMatrix()
|
Compute a Permutation Matrix for Test Statistics |
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bootTEI()
|
Compute a Permutation Matrix of Transcriptome Evolutionary Index (TEI) |
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ecScore()
|
Compute the Hourglass Score for the EarlyConservationTest |
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geom.mean()
|
Geometric Mean |
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harm.mean()
|
Harmonic Mean |
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is.ExpressionSet()
|
Test ExpressionSet Standard |
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omitMatrix()
|
Compute TAI or TDI Profiles Omitting a Given Gene |
|
pMatrix()
|
Compute Partial TAI or TDI Values |
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pMatrixTEI()
|
Compute Partial Transcriptome Evolutionary Index (TEI) Values |
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pStrata()
|
Compute Partial Strata Values |
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pStrataTEI()
|
Compute Partial Transcriptome Evolutionary Index (TEI) Strata Values |
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pTAI()
|
Compute the Phylostratum Contribution to the Global Transcriptome Age Index |
|
pTDI()
|
Compute the Divergence Stratum Contribution to the Global Transcriptome Divergence Index |
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rcpp_boottei_parallel()
|
rcpp_boottei_parallel |
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rcpp_pMatrix_parallel()
|
rcpp_pMatrix_parallel |
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rcpp_pStrata_parallel()
|
rcpp_pStrata_parallel |
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rcpp_tei_parallel()
|
rcpp_tei_parallel |
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reversehourglassScore()
|
Compute the Reverse Hourglass Score for the Reverse Hourglass Test |
|
rhScore()
|
Compute the Hourglass Score for the Reductive Hourglass Test |
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taxid()
|
Retrieve taxonomy categories from NCBI Taxonomy |
|
taxonomy()
|
Retrieving Taxonomic Information of a Query Organism |
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tf()
|
Transform Gene Expression Levels |