myTAI: Perform Evolutionary Transcriptomics Studies

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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.

Author
Hajk-Georg Drost
Date of publication
2016-05-04 13:03:14
Maintainer
Hajk-Georg Drost <hgd23@cam.ac.uk>
License
GPL-3
Version
0.4.0
URLs

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