Package: terapadog 0.99.6

Gionmattia Carancini

terapadog: Translational Efficiency Regulation Analysis using the PADOG Method

This package performs a Gene Set Analysis with the approach adopted by PADOG on the genes that are reported as translationally regulated (ie. exhibit a significant change in TE) by the DeltaTE package. It can be used on its own to see the impact of translation regulation on gene sets, but it is also integrated as an additional analysis method within ReactomeGSA, where results are further contextualised in terms of pathways and directionality of the change.

Authors:Gionmattia Carancini [cre, aut]

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

Bug tracker:https://github.com/gionmattia/terapadog/issues

On BioConductor:terapadog-0.99.6(bioc 3.21)

riboseqtranscriptomicsgenesetenrichmentgeneregulationreactomesoftware

3.90 score 5 exports 117 dependencies

Last updated 8 days agofrom:edf72cebdb. Checks:1 OK, 8 NOTE. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKMar 12 2025
R-4.5-winNOTEMar 12 2025
R-4.5-macNOTEMar 12 2025
R-4.5-linuxNOTEMar 12 2025
R-4.4-winNOTEMar 12 2025
R-4.4-macNOTEMar 12 2025
R-4.4-linuxNOTEMar 12 2025
R-4.3-winNOTEMar 12 2025
R-4.3-macNOTEMar 12 2025

Exports:get_FCsid_converterplotDTAprepareTerapadogDataterapadog

Dependencies:abindAnnotationDbiaskpassbase64encBHBiobaseBiocFileCacheBiocGenericsBiocParallelbiomaRtBiostringsbitbit64blobbslibcachemclicodetoolscolorspacecpp11crayoncrosstalkcurldata.tableDBIdbplyrDelayedArrayDESeq2digestdplyrevaluatefansifarverfastmapfilelockfontawesomeformatRfsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2gluegtablehighrhmshtmltoolshtmlwidgetshttrhttr2IRangesisobandjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlaterlatticelazyevallifecyclelocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmeopensslpillarpkgconfigplogrplotlypngprettyunitsprogresspromisespurrrR6rappdirsRColorBrewerRcppRcppArmadillorlangrmarkdownRSQLiteS4ArraysS4VectorssassscalessnowSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselecttinytexUCSC.utilsutf8vctrsviridisLitewithrxfunxml2XVectoryaml

terapadog: Translational Efficiency Regulation Analysis & Pathway Analysis with Down-weighting of Overlapping Genes

Gionmattia Carancini

Rendered fromterapadog_vignette.Rmdusingknitr::rmarkdownon Mar 12 2025.

Last update: 2025-03-05
Started: 2024-11-25