Package: terapadog
Type: Package
Title: Translational Efficiency Regulation Analysis using the PADOG
        Method
Version: 1.2.0
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
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
biocViews: RiboSeq, Transcriptomics, GeneSetEnrichment, GeneRegulation,
        Reactome, Software
RoxygenNote: 7.3.2
VignetteBuilder: knitr
URL: https://github.com/Gionmattia/terapadog
BugReports: https://github.com/Gionmattia/terapadog/issues
Config/pak/sysreqs: make libicu-dev libpng-dev libxml2-dev libssl-dev
        zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-10-29 15:34:51 UTC
RemoteUrl: https://github.com/bioc/terapadog
RemoteRef: RELEASE_3_22
RemoteSha: c641090d2a802ca59a9ce0bc154d95ab4376e841
NeedsCompilation: no
Packaged: 2026-02-25 08:28:09 UTC; root
Author: Gionmattia Carancini [cre, aut] (ORCID:
    <https://orcid.org/0000-0001-7936-4883>)
Maintainer: Gionmattia Carancini <gionmattia@gmail.com>
Built: R 4.5.2; ; 2026-02-25 08:30:26 UTC; windows
