myTAI: Evolutionary Transcriptomics Analyses
Version 0.5.0

Investigate the evolution of biological processes by capturing evolutionary signatures in transcriptomes. The aim of this tool is to provide a transcriptome analysis environment for answering questions regarding the evolution of biological processes.

Browse man pages Browse package API and functions Browse package files

AuthorHajk-Georg Drost
Date of publication2017-03-14 20:13:25
MaintainerHajk-Georg Drost <hgd23@cam.ac.uk>
LicenseGPL-3
Version0.5.0
URL https://github.com/HajkD/myTAI
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("myTAI")

Man pages

age.apply: Age Category Specific apply Function
bar.colors: Color palette for barplots
bootMatrix: Compute a Permutation Matrix for Test Statistics
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
MatchMap: Match a Phylostratigraphic Map or Divergence Map with a...
omitMatrix: Compute TAI or TDI Profiles Omitting a Given Gene
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...
PlotContribution: Plot Cumuative 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
PlotVars: Plot Variance of Expression Profiles
pMatrix: Compute Partial TAI or TDI Values
pStrata: Compute Partial Strata Values
pTAI: Compute the Phylostratum Contribution to the Global...
pTDI: Compute the Divergence Stratum Contribution to the Global...
RE: Transform to Relative Expression Levels
ReductiveHourglassTest: Perform the Reductive Hourglass Test
REMatrix: Compute a Relative Expression Matrix
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)
tf: Transform Gene Expression Levels
TPI: Compute the Transcriptome Polymorphism Index (TPI)

Functions

CollapseFromTo Source code
CollapseReplicates Man page Source code
CombinatorialSignificance Man page Source code
DiffGenes Man page Source code
DivergenceExpressionSetExample Man page
EarlyConservationTest Man page Source code
EnrichmentTest Man page Source code
Expressed Man page Source code
FlatLineTest Man page Source code
GetColumnIndexFromTo Source code
GroupDiffs Man page Source code
MatchMap Man page Source code
PhyloExpressionSetExample Man page
PlotBarRE Man page Source code
PlotCategoryExpr Man page Source code
PlotContribution Man page Source code
PlotCorrelation Man page Source code
PlotDistribution Man page Source code
PlotEnrichment Man page Source code
PlotGeneSet Man page Source code
PlotGroupDiffs Man page Source code
PlotMeans Man page Source code
PlotMedians Man page Source code
PlotPattern Man page Source code
PlotRE Man page Source code
PlotReplicateQuality Man page Source code
PlotSelectedAgeDistr Man page Source code
PlotSignature Man page Source code
PlotVars Man page Source code
RE Man page Source code
REMatrix Man page Source code
ReductiveHourglassTest Man page Source code
SelectGeneSet Man page Source code
TAI Man page Source code
TDI Man page Source code
TPI Man page Source code
age.apply Man page Source code
bar.colors Man page Source code
bootMatrix Man page Source code
cpp_TAI Source code
cpp_bootMatrix Source code
cpp_geom_mean Source code
cpp_harmonic_mean Source code
cpp_omitMatrix Source code
cpp_pMatrix Source code
cpp_std_error Source code
custom.myTAI.cols Source code
ecScore Man page Source code
geom.mean Man page Source code
get.contingency.tbl Source code
harm.mean Man page Source code
is.ExpressionSet Man page Source code
omitMatrix Man page Source code
pMatrix Man page Source code
pStrata Man page Source code
pTAI Man page Source code
pTDI Man page Source code
pow Source code
quant Source code
re.colors Source code
rhScore Man page Source code
std.error Source code
taxid Man page Source code
taxonomy Man page Source code
tf Man page Source code

Files

inst
inst/CITATION
inst/doc
inst/doc/Enrichment.R
inst/doc/Intermediate.Rmd
inst/doc/Introduction.Rmd
inst/doc/Intermediate.R
inst/doc/Taxonomy.Rmd
inst/doc/Intermediate.html
inst/doc/Expression.R
inst/doc/Advanced.html
inst/doc/Taxonomy.R
inst/doc/Expression.Rmd
inst/doc/Advanced.Rmd
inst/doc/Advanced.R
inst/doc/Introduction.R
inst/doc/Taxonomy.html
inst/doc/Expression.html
inst/doc/Enrichment.Rmd
inst/doc/Introduction.html
inst/doc/Enrichment.html
tests
tests/testthat.R
tests/testthat
tests/testthat/Rplots.pdf
tests/testthat/test-CombinatorialSignificance.R
tests/testthat/test-taxid.R
tests/testthat/test-CollapseReplicates.R
tests/testthat/test-taxonomy.R
tests/testthat/test-ecScore.R
tests/testthat/test-PlotPattern.R
tests/testthat/test-PlotContribution.R
tests/testthat/test-pTAI.R
tests/testthat/test-pMatrix.R
tests/testthat/test-RE.R
tests/testthat/test-PlotEnrichment.R
tests/testthat/test-EarlyConservationTest.R
tests/testthat/test-TAI.R
tests/testthat/test-FlatLineTest.R
tests/testthat/test-PlotRE.R
tests/testthat/test-bootMatrix.R
tests/testthat/test-age.apply.R
tests/testthat/test-PlotMeans.R
tests/testthat/test-TDI.R
tests/testthat/test-rhScore.R
tests/testthat/test-pStrata.R
tests/testthat/test-PlotBarRE.R
tests/testthat/test-MatchMap.R
tests/testthat/test-pTDI.R
tests/testthat/test-DiffGenes.R
tests/testthat/test-omitMatrix.R
tests/testthat/test-ReductiveHourglassTest.R
tests/testthat/test-REMatrix.R
tests/testthat/test-geom.mean.R
tests/testthat/test-Expressed.R
tests/testthat/test-PlotCorrelation.R
tests/testthat/test-PlotGeneSet.R
tests/testthat/test-tf.R
tests/testthat/test-PlotDistribution.R
tests/testthat/test-harm.mean.R
src
src/rcpp_funcs.cpp
src/registerDynamicSymbol.c
src/RcppExports.cpp
NAMESPACE
NEWS.md
data
data/datalist
data/PhyloExpressionSetExample.rda
data/DivergenceExpressionSetExample.rda
R
R/SelectGeneSet.R
R/geom.mean.R
R/custom.myTAI.cols.R
R/PlotReplicateQuality.R
R/PlotEnrichment.R
R/CollapseReplicates.R
R/TPI.R
R/PlotRE.R
R/PlotVars.R
R/PlotDistribution.R
R/PlotBarRE.R
R/FlatLineTest.R
R/pMatrix.R
R/PlotGroupDiffs.R
R/DiffGenes.R
R/TAI.R
R/omitMatrix.R
R/EnrichmentTest.R
R/PlotContribution.R
R/PlotPattern.R
R/bootMatrix.R
R/taxonomy.R
R/GroupDiffs.R
R/PlotCategoryExpr.R
R/PlotSelectedAgeDistr.R
R/RcppExports.R
R/PlotSignature.R
R/base.R
R/pTAI.R
R/ReductiveHourglassTest.R
R/Expressed.R
R/PlotGeneSet.R
R/tf.R
R/is.ExpressionSet.R
R/pTDI.R
R/harm.mean.R
R/PlotMedians.R
R/pStrata.R
R/rhScore.R
R/combinatorialSignificance.R
R/MatchMap.R
R/ecScore.R
R/age.apply.R
R/EarlyConservationTest.R
R/taxid.R
R/TDI.R
R/datasets.R
R/rel_exp.R
R/PlotMeans.R
R/PlotCorrelation.R
vignettes
vignettes/Intermediate.Rmd
vignettes/Introduction.Rmd
vignettes/Figures
vignettes/Figures/Fig3.png
vignettes/Figures/Fig4.pdf
vignettes/Figures/Fig1.pdf
vignettes/Figures/Fig2.png
vignettes/Taxonomy.Rmd
vignettes/Expression.Rmd
vignettes/Advanced.Rmd
vignettes/Enrichment.Rmd
README.md
MD5
build
build/vignette.rds
DESCRIPTION
man
man/age.apply.Rd
man/SelectGeneSet.Rd
man/TDI.Rd
man/TAI.Rd
man/CombinatorialSignificance.Rd
man/PlotVars.Rd
man/rhScore.Rd
man/CollapseReplicates.Rd
man/PlotCorrelation.Rd
man/omitMatrix.Rd
man/PlotCategoryExpr.Rd
man/ReductiveHourglassTest.Rd
man/PlotSelectedAgeDistr.Rd
man/MatchMap.Rd
man/EnrichmentTest.Rd
man/PlotRE.Rd
man/is.ExpressionSet.Rd
man/PlotSignature.Rd
man/taxonomy.Rd
man/PlotBarRE.Rd
man/pStrata.Rd
man/FlatLineTest.Rd
man/PlotPattern.Rd
man/GroupDiffs.Rd
man/pMatrix.Rd
man/PhyloExpressionSetExample.Rd
man/pTDI.Rd
man/TPI.Rd
man/DivergenceExpressionSetExample.Rd
man/harm.mean.Rd
man/PlotMeans.Rd
man/geom.mean.Rd
man/PlotGroupDiffs.Rd
man/tf.Rd
man/bar.colors.Rd
man/PlotGeneSet.Rd
man/bootMatrix.Rd
man/ecScore.Rd
man/PlotMedians.Rd
man/PlotEnrichment.Rd
man/PlotDistribution.Rd
man/Expressed.Rd
man/PlotContribution.Rd
man/PlotReplicateQuality.Rd
man/DiffGenes.Rd
man/taxid.Rd
man/REMatrix.Rd
man/RE.Rd
man/pTAI.Rd
man/EarlyConservationTest.Rd
myTAI documentation built on May 19, 2017, 10:16 a.m.