Package index
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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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TPI()
- Compute the Transcriptome Polymorphism Index (TPI)
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TEI()
- Compute the Transcriptome Evolutionary Index (TEI)
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REMatrix()
- Compute a Relative Expression Matrix
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RE()
- Transform to Relative Expression Levels
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pTAI()
- Compute the Phylostratum Contribution to the Global Transcriptome Age Index
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pTDI()
- Compute the Divergence Stratum Contribution to the Global Transcriptome Divergence Index
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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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GATAI()
- Low level interface function with GATAI
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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 Cumulative 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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PlotSignatureGATAIGeneRemoval()
- Plot evolutionary signatures across transcriptomes after GATAI gene removal
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PlotSignatureTransformed()
- Plot evolutionary signatures across transcriptomes and RNA-seq transformations
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PlotVars()
- Plot Variance of Expression Profiles
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SignatureGATAIGeneRemoval()
- Removed genes after GATAI gene removal and plots of evolutionary signatures across transcriptomes before, after GATAI gene removal and with randomly removed genes
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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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FlatLineTest()
- Perform Flat Line Test
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LateConservationTest()
- Perform Reductive Late Conservation Test
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PairwiseTest()
- Perform Pairwise Difference Test
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ReductiveHourglassTest()
- Perform the Reductive Hourglass Test
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ReverseHourglassTest()
- Perform the Reverse Hourglass Test
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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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DiffGenes()
- Differential Gene Expression Analysis
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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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Expressed()
- Filter for Expressed Genes
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SelectGeneSet()
- Select a Subset of Genes in an ExpressionSet
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PlotReplicateQuality()
- Plot the Quality of Biological Replicates
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GroupDiffs()
- Quantify the significant differences between gene expression distributions of age groups
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taxid()
- Retrieve taxonomy categories from NCBI Taxonomy
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MatchMap()
- Match a Phylostratigraphic Map or Divergence Map with a ExpressionMatrix
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tf()
- Transform Gene Expression Levels
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tfStability()
- Perform Permutation Tests Under Different Transformations
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tfPS()
- Transform Phylostratum Values
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ecScore()
- Compute the Hourglass Score for the EarlyConservationTest
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lcScore()
- Compute the Hourglass Score for the LateConservationTest
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pairScore()
- Compute the Pairwise Difference in TAI Score
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reversehourglassScore()
- Compute the Reverse Hourglass Score for the Reverse Hourglass Test
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rhScore()
- Compute the Hourglass Score for the Reductive Hourglass Test
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age.apply()
- Age Category Specific apply Function
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geom.mean()
- Geometric Mean
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harm.mean()
- Harmonic Mean
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omitMatrix()
- Compute TAI or TDI Profiles Omitting a Given Gene
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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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is_installed_gatai()
- Test whether GATAI is installed on user machine
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DivergenceExpressionSetExample
- An Example DivergenceExpressionSet Data Set
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PhyloExpressionSetExample
- An Example PhyloExpressionSet Data Set