Package: terapadog
Type: Package
Title: Translational Efficiency Regulation Analysis using the PADOG
        Method
Version: 1.0.0
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
git_url: https://git.bioconductor.org/packages/terapadog
git_branch: RELEASE_3_21
git_last_commit: 57e68b9
git_last_commit_date: 2025-04-15
Repository: Bioconductor 3.21
Date/Publication: 2025-04-15
NeedsCompilation: no
Packaged: 2025-04-16 04:10:47 UTC; biocbuild
Author: Gionmattia Carancini [cre, aut] (ORCID:
    <https://orcid.org/0000-0001-7936-4883>)
Maintainer: Gionmattia Carancini <gionmattia@gmail.com>
Built: R 4.5.0; ; 2025-04-16 15:42:15 UTC; windows
