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 |