Package: terapadog
Type: Package
Title: Translational Efficiency Regulation Analysis using the PADOG
        Method
Version: 1.5.6
Authors@R: person("Gionmattia", "Carancini",
            email = "gionmattia@gmail.com",
            role = c("cre", "aut"),
            comment = c(ORCID = "0000-0001-7936-4883"))
Description: 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.
License: GPL-2
Encoding: UTF-8
Imports: DESeq2, KEGGREST, stats, utils, dplyr, plotly, htmlwidgets,
        biomaRt, methods, tidyr, pathview
Suggests: apeglm, BiocStyle, knitr, rmarkdown, testthat
Collate: preprocessing_helpers.R id_converter.R prepareTerapadogData.R
        terapadogBricks.R terapadog.R get_FCs.R assign_Regmode.R
        plotDTA.R pathway_results_viz.R
biocViews: RiboSeq, Transcriptomics, GeneSetEnrichment, GeneRegulation,
        Reactome, Software
VignetteBuilder: knitr
URL: https://github.com/Gionmattia/terapadog
BugReports: https://github.com/Gionmattia/terapadog/issues
Config/roxygen2/version: 8.1.0
Config/pak/sysreqs: cmake make libicu-dev libpng-dev libuv1-dev
        libxml2-dev libssl-dev zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-09-21 13:24:52 UTC
RemoteUrl: https://github.com/bioc/terapadog
RemoteRef: HEAD
RemoteSha: f5f1311b02f943b6ff00c53016f998a632acdbb2
NeedsCompilation: no
Packaged: 2026-09-22 00:24:24 UTC; root
Author: Gionmattia Carancini [cre, aut] (ORCID:
    <https://orcid.org/0000-0001-7936-4883>)
Maintainer: Gionmattia Carancini <gionmattia@gmail.com>