myTAI: Evolutionary Transcriptomics Analyses

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.

AuthorHajk-Georg Drost
Date of publication2017-03-14 20:13:25
MaintainerHajk-Georg Drost <hgd23@cam.ac.uk>
LicenseGPL-3
Version0.5.0
https://github.com/HajkD/myTAI

View on CRAN

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

age.apply Man page
bar.colors Man page
bootMatrix Man page
CollapseReplicates Man page
CombinatorialSignificance Man page
DiffGenes Man page
DivergenceExpressionSetExample Man page
EarlyConservationTest Man page
ecScore Man page
EnrichmentTest Man page
Expressed Man page
FlatLineTest Man page
geom.mean Man page
GroupDiffs Man page
harm.mean Man page
is.ExpressionSet Man page
MatchMap Man page
omitMatrix Man page
PhyloExpressionSetExample Man page
PlotBarRE Man page
PlotCategoryExpr Man page
PlotContribution Man page
PlotCorrelation Man page
PlotDistribution Man page
PlotEnrichment Man page
PlotGeneSet Man page
PlotGroupDiffs Man page
PlotMeans Man page
PlotMedians Man page
PlotPattern Man page
PlotRE Man page
PlotReplicateQuality Man page
PlotSelectedAgeDistr Man page
PlotSignature Man page
PlotVars Man page
pMatrix Man page
pStrata Man page
pTAI Man page
pTDI Man page
RE Man page
ReductiveHourglassTest Man page
REMatrix Man page
rhScore Man page
SelectGeneSet Man page
TAI Man page
taxid Man page
taxonomy Man page
TDI Man page
tf Man page
TPI Man page

Files

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.