myTAI: Perform Evolutionary Transcriptomics Studies

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 publication2016-05-04 13:03:14
MaintainerHajk-Georg Drost <hgd23@cam.ac.uk>
LicenseGPL-3
Version0.4.0
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 the 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 the 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 the Mean Relative Expression Levels as Barplot

PlotCategoryExpr: Plot the Expression Levels of each Age or Divergence Category...

PlotContribution: Plot the Phylostratum or Divergence Stratum Contribution to...

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 the Mean Expression Profiles of Phylostrata or...

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

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

Files in this package

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/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/PlotReplicateQuality.R myTAI/R/PlotEnrichment.R myTAI/R/CollapseReplicates.R myTAI/R/PlotRE.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/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/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/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/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/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/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/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.

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