All functions

CollapseReplicates()

Combine Replicates in an ExpressionSet

CombinatorialSignificance()

Compute the Statistical Significance of Each Replicate Combination

DiffGenes()

Differential Gene Expression Analysis

DivergenceExpressionSetExample

An Example DivergenceExpressionSet Data Set

EarlyConservationTest()

Perform Reductive Early Conservation Test

EnrichmentTest()

Phylostratum or Divergence Stratum Enrichment of a given Gene Set based on Fisher's Test

Expressed()

Filter for Expressed Genes

FlatLineTest()

Perform Flat Line Test

GroupDiffs()

Quantify the significant differences between gene expression distributions of age groups

MatchMap()

Match a Phylostratigraphic Map or Divergence Map with a ExpressionMatrix

PhyloExpressionSetExample

An Example PhyloExpressionSet Data Set

PlotBarRE()

Plot Mean Relative Expression Levels as Barplot

PlotCIRatio()

Plot Transcriptome Index using bootstrapping and confidence intervals

PlotCategoryExpr()

Plot the Expression Levels of each Age or Divergence Category as Boxplot, Violinplot, or Dotplot

PlotContribution()

Plot Cumuative Transcriptome Index

PlotCorrelation()

Plot the Correlation Between Phylostrata and Divergence Strata

PlotDistribution()

Plot the Frequency Distribution of Phylostrata or Divergence Strata

PlotEnrichment()

Plot the Phylostratum or Divergence Stratum Enrichment of a given Gene Set

PlotGeneSet()

Plot the Expression Profiles of a Gene Set

PlotGroupDiffs()

Plot the significant differences between gene expression distributions of PS or DS groups

PlotMeans()

Plot Mean Expression Profiles

PlotMedians()

Plot Median Expression Profiles

PlotPattern()

Plot the Transcriptome Age Index or Transcriptome Divergence Index

PlotRE()

Plot Relative Expression Levels

PlotReplicateQuality()

Plot the Quality of Biological Replicates

PlotSelectedAgeDistr()

Plot the PS or DS distribution of a selected set of genes

PlotSignature()

Plot evolutionary signatures across transcriptomes

PlotVars()

Plot Variance of Expression Profiles

RE()

Transform to Relative Expression Levels

REMatrix()

Compute a Relative Expression Matrix

ReductiveHourglassTest()

Perform the Reductive Hourglass Test

ReverseHourglassTest()

Perform the Reverse Hourglass Test

SelectGeneSet()

Select a Subset of Genes in an ExpressionSet

TAI()

Compute the Transcriptome Age Index (TAI)

TDI()

Compute the Transcriptome Divergence Index (TDI)

TEI()

Compute the Transcriptome Evolutionary Index (TEI)

TPI()

Compute the Transcriptome Polymorphism Index (TPI)

age.apply()

Age Category Specific apply Function

bar.colors()

Color palette for barplots

bootMatrix()

Compute a Permutation Matrix for Test Statistics

bootTEI()

Compute a Permutation Matrix of Transcriptome Evolutionary Index (TEI)

ecScore()

Compute the Hourglass Score for the EarlyConservationTest

geom.mean()

Geometric Mean

harm.mean()

Harmonic Mean

is.ExpressionSet()

Test ExpressionSet Standard

omitMatrix()

Compute TAI or TDI Profiles Omitting a Given Gene

pMatrix()

Compute Partial TAI or TDI Values

pMatrixTEI()

Compute Partial Transcriptome Evolutionary Index (TEI) Values

pStrata()

Compute Partial Strata Values

pStrataTEI()

Compute Partial Transcriptome Evolutionary Index (TEI) Strata Values

pTAI()

Compute the Phylostratum Contribution to the Global Transcriptome Age Index

pTDI()

Compute the Divergence Stratum Contribution to the Global Transcriptome Divergence Index

rcpp_boottei_parallel()

rcpp_boottei_parallel

rcpp_pMatrix_parallel()

rcpp_pMatrix_parallel

rcpp_pStrata_parallel()

rcpp_pStrata_parallel

rcpp_tei_parallel()

rcpp_tei_parallel

reversehourglassScore()

Compute the Reverse Hourglass Score for the Reverse Hourglass Test

rhScore()

Compute the Hourglass Score for the Reductive Hourglass Test

taxid()

Retrieve taxonomy categories from NCBI Taxonomy

taxonomy()

Retrieving Taxonomic Information of a Query Organism

tf()

Transform Gene Expression Levels