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... |
CollapseReplicates | Combine Replicates in an ExpressionSet |
CombinatorialSignificance | Compute the Statistical Significance of Each Replicate... |
DiffGenes | Differential Gene Expression Analysis |
DivergenceExpressionSetExample | An Example DivergenceExpressionSet Data Set |
EarlyConservationTest | Perform Reductive Early Conservation Test |
ecScore | Compute the Hourglass Score for the EarlyConservationTest |
EnrichmentTest | Phylostratum or Divergence Stratum Enrichment of a given Gene... |
Expressed | Filter for Expressed Genes |
FlatLineTest | Perform Flat Line Test |
geom.mean | Geometric Mean |
GroupDiffs | Quantify the significant differences between gene expression... |
harm.mean | Harmonic Mean |
is.ExpressionSet | Test ExpressionSet Standard |
LateConservationTest | Perform Reductive Late Conservation Test |
lcScore | Compute the Hourglass Score for the LateConservationTest |
MatchMap | Match a Phylostratigraphic Map or Divergence Map with a... |
omitMatrix | Compute TAI or TDI Profiles Omitting a Given Gene |
pairScore | Compute the Pairwise Difference in TAI Score |
PairwiseTest | Perform Pairwise Difference Test |
PhyloExpressionSetExample | An Example PhyloExpressionSet Data Set |
PlotBarRE | Plot Mean Relative Expression Levels as Barplot |
PlotCategoryExpr | Plot the Expression Levels of each Age or Divergence Category... |
PlotCIRatio | Plot Transcriptome Index using bootstrapping and confidence... |
PlotContribution | Plot Cumulative Transcriptome Index |
PlotCorrelation | Plot the Correlation Between Phylostrata and Divergence... |
PlotDistribution | Plot the Frequency Distribution of Phylostrata or Divergence... |
PlotEnrichment | Plot the Phylostratum or Divergence Stratum Enrichment of a... |
PlotGeneSet | Plot the Expression Profiles of a Gene Set |
PlotGroupDiffs | Plot the significant differences between gene expression... |
PlotMeans | Plot Mean Expression Profiles |
PlotMedians | Plot Median Expression Profiles |
PlotPattern | Plot the Transcriptome Age Index or Transcriptome Divergence... |
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 |
PlotSignatureTransformed | Plot evolutionary signatures across transcriptomes and... |
PlotVars | Plot Variance of Expression Profiles |
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... |
pTAI | Compute the Phylostratum Contribution to the Global... |
pTDI | Compute the Divergence Stratum Contribution to the Global... |
rcpp_boottei_parallel | rcpp_boottei_parallel |
rcpp_pMatrix_parallel | rcpp_pMatrix_parallel |
rcpp_pStrata_parallel | rcpp_pStrata_parallel |
rcpp_tei_parallel | rcpp_tei_parallel |
RE | Transform to Relative Expression Levels |
ReductiveHourglassTest | Perform the Reductive Hourglass Test |
REMatrix | Compute a Relative Expression Matrix |
reversehourglassScore | Compute the Reverse Hourglass Score for the Reverse Hourglass... |
ReverseHourglassTest | Perform the Reverse Hourglass Test |
rhScore | Compute the Hourglass Score for the Reductive Hourglass Test |
SelectGeneSet | Select a Subset of Genes in an ExpressionSet |
TAI | Compute the Transcriptome Age Index (TAI) |
taxid | Retrieve taxonomy categories from NCBI Taxonomy |
taxonomy | Retrieving Taxonomic Information of a Query Organism |
TDI | Compute the Transcriptome Divergence Index (TDI) |
TEI | Compute the Transcriptome Evolutionary Index (TEI) |
tf | Transform Gene Expression Levels |
tfPS | Transform Phylostratum Values |
tfStability | Perform Permutation Tests Under Different Transformations |
TPI | Compute the Transcriptome Polymorphism Index (TPI) |
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