Package: myTAI 2.0.0

Hajk-Georg Drost

myTAI: Evolutionary Transcriptomics

Investigate the evolution of biological processes by capturing evolutionary signatures in transcriptomes (Drost et al. (2018) <doi:10.1093/bioinformatics/btx835>). This package aims to provide a transcriptome analysis environment to quantify the average evolutionary age of genes contributing to a transcriptome of interest.

Authors:Hajk-Georg Drost [aut, cre], Jaruwatana Sodai Lotharukpong [aut, ctb], Nikola Kalábová [aut, ctb], Filipa Martins Costa [aut, ctb], Kristian K Ullrich [aut, ctb], Stefan Manolache [aut, ctb]

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myTAI.pdf |myTAI.html✨
myTAI/json (API)
NEWS

# Install 'myTAI' in R:
install.packages('myTAI', repos = c('https://drostlab.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/drostlab/mytai/issues

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:

On CRAN:

biological-processesconservationevo-devoevolutionevolutionary-transcriptomicsexpression-profilesgene-expressiongene-setsmytaistudies-transcriptomestranscriptome

8.87 score 41 stars 63 scripts 173 downloads 4 mentions 73 exports 128 dependencies

Last updated 11 hours agofrom:a718cf441d. Checks:OK: 2 WARNING: 6 ERROR: 1. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 21 2024
R-4.5-win-x86_64WARNINGNov 21 2024
R-4.5-linux-x86_64WARNINGNov 21 2024
R-4.4-win-x86_64WARNINGNov 21 2024
R-4.4-mac-x86_64ERRORNov 21 2024
R-4.4-mac-aarch64WARNINGNov 21 2024
R-4.3-win-x86_64WARNINGNov 21 2024
R-4.3-mac-aarch64WARNINGNov 21 2024
R-4.3-mac-x86_64OKOct 08 2024

Exports:age.applybar.colorsbootMatrixbootTEICollapseReplicatesCombinatorialSignificanceDiffGenesEarlyConservationTestecScoreEnrichmentTestExpressedFlatLineTestGATAIgeom.meanGroupDiffsharm.meanis_installed_gataiis.ExpressionSetLateConservationTestlcScoreMatchMapomitMatrixpairScorePairwiseTestPlotBarREPlotCategoryExprPlotCIRatioPlotContributionPlotCorrelationPlotDistributionPlotEnrichmentPlotGeneSetPlotGroupDiffsPlotMeansPlotMediansPlotPatternPlotREPlotReplicateQualityPlotSelectedAgeDistrPlotSignaturePlotSignatureGATAIGeneRemovalPlotSignatureGeneQuantilesPlotSignatureMultiplePlotSignatureTransformedPlotVarspMatrixpMatrixTEIpStratapStrataTEIpTAIpTDIrcpp_boottei_parallelrcpp_pMatrix_parallelrcpp_pStrata_parallelrcpp_tei_parallelREReductiveHourglassTestREMatrixreversehourglassScoreReverseHourglassTestrhScoreSelectGeneSetSignatureGATAIGeneRemovalTAItaxidTDITEItftfPStfStabilityTopExpressionGenesTopVarianceGenesTPI

Dependencies:abindaskpassbackportsBHBiobaseBiocGenericsBiocParallelbitbit64bootbroomcarcarDataclicliprcodetoolscolorspacecommonmarkcorrplotcowplotcpp11crayoncurlDelayedArrayDerivDESeq2doBydoParalleldplyrfansifarverfitdistrplusforeachformatRFormulafutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2ggpubrggrepelggsciggsignifggtextgluegridExtragridtextgtablehmshttrIRangesisobanditeratorsjpegjsonlitelabelinglambda.rlatticelifecyclelme4locfitmagrittrmarkdownMASSMatrixMatrixGenericsMatrixModelsmatrixStatsmgcvmicrobenchmarkmimeminqamodelrmunsellnlmenloptrnnetnortestnumDerivopensslpbkrtestpillarpkgconfigplyrpngpolynomprettyunitsprogresspurrrquantregR6RColorBrewerRcppRcppArmadilloRcppEigenRcppThreadreadrreshape2rlangrstatixS4ArraysS4VectorsscalessnowSparseArraySparseMstringistringrSummarizedExperimentsurvivalsystibbletidyrtidyselecttzdbUCSC.utilsutf8vctrsviridisLitevroomwithrxfunxml2XVectorzlibbioc

Advanced Phylotranscriptomics Analyses

Rendered fromAdvanced.Rmdusingknitr::rmarkdownon Nov 21 2024.

Last update: 2023-08-16
Started: 2014-10-10

Discussing Genomic Phylostratigraphy

Rendered fromPhylostratigraphy.Rmdusingknitr::rmarkdownon Nov 21 2024.

Last update: 2024-10-03
Started: 2021-09-07

Enrichment Analyses

Rendered fromEnrichment.Rmdusingknitr::rmarkdownon Nov 21 2024.

Last update: 2024-10-03
Started: 2015-06-05

Gene Expression Analysis with myTAI

Rendered fromExpression.Rmdusingknitr::rmarkdownon Nov 21 2024.

Last update: 2024-10-03
Started: 2015-06-13

Intermediate Phylotranscriptomics Analyses

Rendered fromIntermediate.Rmdusingknitr::rmarkdownon Nov 21 2024.

Last update: 2024-10-03
Started: 2014-10-04

Introduction to the myTAI package

Rendered fromIntroduction.Rmdusingknitr::rmarkdownon Nov 21 2024.

Last update: 2024-10-03
Started: 2014-10-04

Readme and manuals

Help Manual

Help pageTopics
Age Category Specific apply Functionage.apply
Compute a Permutation Matrix for Test StatisticsbootMatrix
Compute a Permutation Matrix of Transcriptome Evolutionary Index (TEI)bootTEI
Combine Replicates in an ExpressionSetCollapseReplicates
Compute the Statistical Significance of Each Replicate CombinationCombinatorialSignificance
Differential Gene Expression AnalysisDiffGenes
An Example DivergenceExpressionSet Data SetDivergenceExpressionSetExample
Perform Reductive Early Conservation TestEarlyConservationTest
Compute the Hourglass Score for the EarlyConservationTestecScore
Phylostratum or Divergence Stratum Enrichment of a given Gene Set based on Fisher's TestEnrichmentTest
Filter for Expressed GenesExpressed
Perform Flat Line TestFlatLineTest
Low level interface function with GATAIGATAI
Geometric Meangeom.mean
Quantify the significant differences between gene expression distributions of age groupsGroupDiffs
Harmonic Meanharm.mean
Test whether GATAI is installed on user machineis_installed_gatai
Perform Reductive Late Conservation TestLateConservationTest
Compute the Hourglass Score for the LateConservationTestlcScore
Match a Phylostratigraphic Map or Divergence Map with a ExpressionMatrixMatchMap
Compute TAI or TDI Profiles Omitting a Given GeneomitMatrix
Compute the Pairwise Difference in TAI ScorepairScore
Perform Pairwise Difference TestPairwiseTest
An Example PhyloExpressionSet Data SetPhyloExpressionSetExample
Plot Mean Relative Expression Levels as BarplotPlotBarRE
Plot the Expression Levels of each Age or Divergence Category as Boxplot, Violinplot, or DotplotPlotCategoryExpr
Plot Transcriptome Index using bootstrapping and confidence intervalsPlotCIRatio
Plot Cumulative Transcriptome IndexPlotContribution
Plot the Correlation Between Phylostrata and Divergence StrataPlotCorrelation
Plot the Frequency Distribution of Phylostrata or Divergence StrataPlotDistribution
Plot the Phylostratum or Divergence Stratum Enrichment of a given Gene SetPlotEnrichment
Plot the Expression Profiles of a Gene SetPlotGeneSet
Plot the significant differences between gene expression distributions of PS or DS groupsPlotGroupDiffs
Plot Mean Expression ProfilesPlotMeans
Plot Median Expression ProfilesPlotMedians
Plot the Transcriptome Age Index or Transcriptome Divergence IndexPlotPattern
Plot Relative Expression LevelsPlotRE
Plot the Quality of Biological ReplicatesPlotReplicateQuality
Plot the PS or DS distribution of a selected set of genesPlotSelectedAgeDistr
Plot evolutionary signatures across transcriptomesPlotSignature
Plot evolutionary signatures across transcriptomes after GATAI gene removalPlotSignatureGATAIGeneRemoval
Plot evolutionary signatures across transcriptomes, removing top level genesPlotSignatureGeneQuantiles
Plot evolutionary signatures across transcriptomes, for multiple expression setsPlotSignatureMultiple
Plot evolutionary signatures across transcriptomes and RNA-seq transformationsPlotSignatureTransformed
Plot Variance of Expression ProfilesPlotVars
Compute Partial TAI or TDI ValuespMatrix
Compute Partial Transcriptome Evolutionary Index (TEI) ValuespMatrixTEI
Compute Partial Strata ValuespStrata
Compute Partial Transcriptome Evolutionary Index (TEI) Strata ValuespStrataTEI
Compute the Phylostratum Contribution to the Global Transcriptome Age IndexpTAI
Compute the Divergence Stratum Contribution to the Global Transcriptome Divergence IndexpTDI
rcpp_boottei_parallelrcpp_boottei_parallel
rcpp_pMatrix_parallelrcpp_pMatrix_parallel
rcpp_pStrata_parallelrcpp_pStrata_parallel
rcpp_tei_parallelrcpp_tei_parallel
Transform to Relative Expression LevelsRE
Perform the Reductive Hourglass TestReductiveHourglassTest
Compute a Relative Expression MatrixREMatrix
Compute the Reverse Hourglass Score for the Reverse Hourglass TestreversehourglassScore
Perform the Reverse Hourglass TestReverseHourglassTest
Compute the Hourglass Score for the Reductive Hourglass TestrhScore
Select a Subset of Genes in an ExpressionSetSelectGeneSet
Removed genes after GATAI gene removal and plots of evolutionary signatures across transcriptomes before, after GATAI gene removal and with randomly removed genesSignatureGATAIGeneRemoval
Compute the Transcriptome Age Index (TAI)TAI
Retrieve taxonomy categories from NCBI Taxonomytaxid
Compute the Transcriptome Divergence Index (TDI)TDI
Compute the Transcriptome Evolutionary Index (TEI)TEI
Transform Gene Expression Levelstf
Transform Phylostratum ValuestfPS
Perform Permutation Tests Under Different TransformationstfStability
Top quantile expression genesTopExpressionGenes
Top quantile expression-variance genesTopVarianceGenes
Compute the Transcriptome Polymorphism Index (TPI)TPI