{ "_id": "6a1af4b91d7bb097a09f8d59", "Package": "terapadog", "Type": "Package", "Title": "Translational Efficiency Regulation Analysis using the PADOG\nMethod", "Version": "1.5.0", "Authors@R": "person(\"Gionmattia\", \"Carancini\",\nemail = \"gionmattia@gmail.com\",\nrole = c(\"cre\", \"aut\"),\ncomment = c(ORCID = \"0000-0001-7936-4883\"))", "Description": "This package performs a Gene Set Analysis with the\napproach adopted by PADOG on the genes that are reported as\ntranslationally regulated (ie. exhibit a significant change in\nTE) by the DeltaTE package. It can be used on its own to see\nthe impact of translation regulation on gene sets, but it is\nalso integrated as an additional analysis method within\nReactomeGSA, where results are further contextualised in terms\nof pathways and directionality of the change.", "License": "GPL-2", "Encoding": "UTF-8", "Collate": "preprocessing_helpers.R id_converter.R prepareTerapadogData.R\nterapadogBricks.R terapadog.R get_FCs.R assign_Regmode.R\nplotDTA.R", "biocViews": "RiboSeq, Transcriptomics, GeneSetEnrichment, GeneRegulation,\nReactome, Software", "RoxygenNote": "7.3.2", "VignetteBuilder": "knitr", "URL": "https://github.com/Gionmattia/terapadog", "BugReports": "https://github.com/Gionmattia/terapadog/issues", "Config/pak/sysreqs": "cmake make libicu-dev libpng-dev libuv1-dev\nlibxml2-dev libssl-dev zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 13:04:33 UTC", "RemoteUrl": "https://github.com/bioc/terapadog", "RemoteRef": "HEAD", "RemoteSha": "54d05ead9b262b688484fa0371729e890355c89e", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-30 09:44:53 UTC", "User": "root" }, "Author": "Gionmattia Carancini [cre, aut] (ORCID:\n)", "Maintainer": "Gionmattia Carancini ", "MD5sum": "b274d80f30c839f375ffa250784c5d95", "_user": "bioc", "_type": "src", "_file": "terapadog_1.5.0.tar.gz", "_fileid": "a6910ec56ec7a56b737bba1a9f5e3858984417961ffcd8c8f2cc5571c9e7e8e8", "_filesize": 1458942, "_sha256": "a6910ec56ec7a56b737bba1a9f5e3858984417961ffcd8c8f2cc5571c9e7e8e8", "_created": "2026-05-30T09:44:53.000Z", "_published": "2026-05-30T14:31:21.598Z", "_jobs": [ { "job": 78640524093, "time": 195, "config": "bioc-checks", "r": "4.6.0", "check": "NOTE", "artifact": "7307459382" }, { "job": 78640524091, "time": 530, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7307488404" }, { "job": 78640524094, "time": 572, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7307491575" }, { "job": 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"_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/terapadog", "_commit": { "id": "54d05ead9b262b688484fa0371729e890355c89e", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777381473 }, "_maintainer": { "name": "Gionmattia Carancini", "email": "gionmattia@gmail.com", "login": "gionmattia", "description": "", "uuid": 98411936, "orcid": "0000-0001-7936-4883" }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "DESeq2", "role": "Imports" }, { "package": "KEGGREST", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "dplyr", "role": "Imports" }, { "package": "plotly", "role": "Imports" }, { "package": "htmlwidgets", "role": "Imports" }, { "package": "biomaRt", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "apeglm", "role": "Suggests" }, { "package": 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The output is a dataframe with the FC in mRNA counts, RIBO counts or TE between the conditions in exam.", "topics": [ "get_FCs" ] }, { "page": "id_converter", "title": "Convert the human gene identifier (hgnc_symbol or ensembl_gene_id) to entrezgene_id format for the analysis.", "topics": [ "id_converter" ] }, { "page": "plotDTA", "title": "This function will plot an interactive html plot of the results of get_FCs.R That is to say, a plot of the genes undergoing translational regulation, coloured by RegMode. Genes whose RegMode was Undeterminable or Undetermined are omitted.", "topics": [ "plotDTA" ] }, { "page": "prepareTerapadogData", "title": "Prepare Data by Loading and Validating RNA, RIBO Counts, and Metadata. This function reads RNA and RIBO count files, checks input data validity and merges them into a single numerical matrix (expression.data). It also prepares the metatadata needed by padog (exp_de).", "topics": [ "prepareTerapadogData" ] }, { "page": "terapadog", "title": "Performs the main Gene Set Enrichement Analysis, by applying a modified version of the PADOG algorithm to genes undergoing changes in TE.", "topics": [ "terapadog" ] } ], "_rundeps": [ "abind", "AnnotationDbi", "askpass", "base64enc", "BH", "Biobase", "BiocFileCache", "BiocGenerics", "BiocParallel", "biomaRt", "Biostrings", "bit", "bit64", "blob", "bslib", "cachem", "cli", "codetools", "cpp11", "crayon", "crosstalk", "curl", "data.table", "DBI", "dbplyr", "DelayedArray", "DESeq2", "digest", "dplyr", "evaluate", "farver", "fastmap", "filelock", "fontawesome", "formatR", "fs", "futile.logger", "futile.options", "generics", "GenomicRanges", "ggplot2", "glue", "gtable", "highr", "hms", "htmltools", "htmlwidgets", "httr", "httr2", "IRanges", "isoband", "jquerylib", "jsonlite", "KEGGREST", "knitr", "labeling", "lambda.r", "later", "lattice", "lazyeval", 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its Gene Set Analysis", "Suggested Reading", "Installation & Loading", "Analysis Walktrough", "Understanding the results", "Input data: Formatting and Extension", "prepareTerapadogData()", "id_converter()", "terapadog()", "get_FCs()", "plotDTA()", "References", "Ackwoledgements", "SessionInfo" ], "created": "2024-11-25 14:45:38", "modified": "2025-03-05 16:40:42", "commits": 4 } ], "_score": 3.3010299956639813, "_indexed": true, "_nocasepkg": "terapadog", "_universes": [ "bioc", "gionmattia" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.5.0", "date": "2026-05-30T10:17:08.000Z", "distro": "noble", "commit": "54d05ead9b262b688484fa0371729e890355c89e", "fileid": "d8d3ffae81f0d1054c54dbf0a4048aa76cd63362fe8d1cbbb089b2df8cfaf55e", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676625405" }, { "r": "4.6.0", "os": "linux", "version": "1.5.0", "date": "2026-05-30T10:17:41.000Z", "distro": "noble", "commit": 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