{ "_id": "6a1f1d52b401979e7341fb53", "Package": "phoenics", "Type": "Package", "Title": "Pathways Longitudinal and Differential Analysis in Metabolomics", "Version": "0.6", "Date": "2025-08-19", "Authors@R": "c(person(\"Camille\", \"Guilmineau\", role = \"aut\", \nemail = \"camille.guilmineau@inrae.fr\"),\nperson(\"Remi\", \"Servien\", role = c(\"aut\", \"cre\"),\nemail = \"remi.servien@inrae.fr\",\ncomment = c(ORCID = \"0000-0003-1270-1843\")),\nperson(\"Nathalie\", \"Vialaneix\", role = \"aut\",\nemail = \"nathalie.vialaneix@inrae.fr\",\ncomment = c(ORCID = \"0000-0003-1156-0639\")))", "Maintainer": "Remi Servien ", "Description": "Perform a differential analysis at pathway level based on\nmetabolite quantifications and information on pathway\nmetabolite composition. The method, described in Guilmineau et\nal (2025) is based on a\nPrincipal Component Analysis step and on a linear mixed model.\nAutomatic query of metabolic pathways is also implemented.", "License": "GPL-3", "BugReports": "https://forge.inrae.fr/panoramics/phoenics/-/issues", "Encoding": "UTF-8", "NeedsCompilation": "no", "URL": "https://forge.inrae.fr/panoramics/phoenics", "LazyData": "true", "RoxygenNote": "7.3.2", "VignetteBuilder": "knitr", "Language": "en-US", "Packaged": { "Date": "2026-05-16 08:41:46 UTC", "User": "root" }, "Author": "Camille Guilmineau [aut], Remi Servien [aut, cre] (ORCID:\n), Nathalie Vialaneix\n[aut] (ORCID: )", "Config/pak/sysreqs": "cmake make libicu-dev libuv1-dev", "Repository": "https://r-serv.r-universe.dev", "Date/Publication": "2025-08-19 08:40:08 UTC", "RemoteUrl": "https://github.com/cran/phoenics", "RemoteRef": "HEAD", "RemoteSha": "d2537f0f96478d5f961848606ccc0ef01aa8b4c8", "MD5sum": "4008f93709a30ab84a96c19c81d07dbf", "_user": "r-serv", "_type": "src", "_file": "phoenics_0.6.tar.gz", "_fileid": "29ba02d0359478295d4b78b11ec2f54c09524e35065f9c0c6fcad64a1c2404be", "_filesize": 494813, "_sha256": "29ba02d0359478295d4b78b11ec2f54c09524e35065f9c0c6fcad64a1c2404be", "_created": "2026-05-16T08:41:46.000Z", "_published": "2026-06-02T18:13:38.424Z", "_distro": "noble", "_jobs": [ { "job": 79140431823, "time": 210, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7032055441" }, { "job": 79140432369, "time": 198, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7032054129" }, { "job": 79140432214, "time": 204, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7032050816" }, { "job": 79140431982, "time": 172, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7032048078" }, { "job": 79140431082, "time": 230, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7032031946" }, { "job": 79140431073, "time": 144, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7366126246" }, { "job": 79140432359, "time": 142, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7032047544" }, { "job": 79140433155, "time": 140, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7032047644" }, { "job": 79140432204, "time": 141, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7032047543" } ], "_buildurl": "https://github.com/r-universe/r-serv/actions/runs/25957510094", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/cran/phoenics", "_commit": { "id": "d2537f0f96478d5f961848606ccc0ef01aa8b4c8", "author": "Remi Servien ", "committer": "cran-robot ", "message": "version 0.6\n", "time": 1755592808 }, "_maintainer": { "name": "Remi Servien", "email": "remi.servien@inrae.fr", "login": "r-serv", "uuid": 249908442, "orcid": "0000-0003-1270-1843" }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.0.0", "role": "Depends" }, { "package": "lme4", "role": "Imports" }, { "package": "blme", "role": "Imports" }, { "package": "tibble", "role": "Imports" }, { "package": "FactoMineR", "role": "Imports" }, { "package": "factoextra", "role": "Imports" }, { "package": "tidyr", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "KEGGREST", "role": "Suggests" } ], "_owner": "cran", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-34", "n": 1 } ], "_tags": [ { "name": "0.6", "date": "2025-08-19" } ], "_stars": 0, "_contributors": [ { "user": "r-serv", "count": 1, "uuid": 249908442 } ], "_userbio": { "uuid": 249908442, "type": "user", "name": "R-serv" }, "_downloads": { "count": 183, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/phoenics" }, "_searchresults": 0, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "extra/phoenics.html", "manual.pdf" ], "_realowner": "r-serv", "_cranurl": false, "_releases": [ { "version": "0.1", "date": "2024-05-22" }, { "version": "0.2", "date": "2024-06-27" }, { "version": "0.3", "date": "2024-07-22" }, { "version": "0.4", "date": "2024-12-12" }, { "version": "0.5", "date": "2025-01-29" }, { "version": "0.6", "date": "2025-08-19" } ], "_exports": [ "adjust_pval", "extract", "from_ASICS_to_PHOENICS", "overlap_coefficient", "pathway_search", "test_pathway" ], "_datasets": [ { "name": "design", "title": "Dataset \"MTBLS422\"", "object": "MTBLS422", "class": [ "data.frame" ], "fields": [ "Id", "Age", "Treatment", "Mouse" ], "rows": 11, "table": true, "tojson": true }, { "name": "pathways", "title": "Dataset \"MTBLS422\"", "object": "MTBLS422", "class": [ "data.frame" ], "fields": [ "metabolite_code", "metabolite_name", "pathway_code", "pathway_name" ], "rows": 11, "table": true, "tojson": true }, { "name": "quantif", "title": "Dataset \"MTBLS422\"", "object": "MTBLS422", "class": [ "data.frame" ], "fields": [ "1071", "1151", "1231", "1281", "1371", "1531", "1681", "1751", "2081", "2161", "2311" ], "rows": 10, "table": true, "tojson": true } ], "_help": [ { "page": "from_ASICS_to_PHOENICS", "title": "Prepare quantification data from ASICS outputs", "topics": [ "from_ASICS_to_PHOENICS" ] }, { "page": "MTBLS422", "title": "Dataset \"MTBLS422\"", "topics": [ "design", "MTBLS422", "pathways", "quantif" ] }, { "page": "overlap_coefficient", "title": "Calculate overlap coefficient between pathways", "topics": [ "overlap_coefficient" ] }, { "page": "pathway_search", "title": "Query KEGG pathways for a given set of metabolites", "topics": [ "pathway_search" ] }, { "page": "pathwayRes", "title": "Class pathwayRes", "topics": [ "adjust_pval", "adjust_pval.pathwayRes", "extract", "extract.pathwayRes", "head.pathwayRes", "pathwayRes", "plot.pathwayRes", "print.pathwayRes", "summary.pathwayRes" ] }, { "page": "test_pathway", "title": "Pathway differential analysis based on longitudinal metabolomics data", "topics": [ "test_pathway" ] } ], "_rundeps": [ "abind", "backports", "base64enc", "blme", "boot", "broom", "bslib", "cachem", "car", "carData", "cli", "cluster", "colorspace", "corrplot", "cowplot", "cpp11", "crosstalk", "dendextend", "Deriv", "digest", "doBy", "dplyr", "DT", "ellipse", "emmeans", "estimability", "evaluate", "factoextra", "FactoMineR", "farver", "fastmap", "flashClust", "fontawesome", "forecast", "Formula", "fracdiff", "fs", "generics", "ggplot2", "ggpubr", "ggrepel", "ggsci", "ggsignif", "glue", "gridExtra", "gtable", "highr", "htmltools", "htmlwidgets", "isoband", "jquerylib", "jsonlite", "knitr", "labeling", "later", "lattice", "lazyeval", "leaps", "lifecycle", "lme4", "lmtest", "magrittr", "MASS", "Matrix", "MatrixModels", "memoise", "mgcv", "microbenchmark", "mime", "minqa", "modelr", "multcompView", "mvtnorm", "nlme", "nloptr", "nnet", "numDeriv", "otel", "pbkrtest", "pillar", "pkgconfig", "polynom", "promises", "purrr", "quantreg", "R6", "rappdirs", "rbibutils", "RColorBrewer", "Rcpp", "RcppArmadillo", "RcppEigen", "Rdpack", "reformulas", "rlang", "rmarkdown", "rstatix", "S7", "sass", "scales", "scatterplot3d", "SparseM", "stringi", "stringr", "survival", "tibble", "tidyr", "tidyselect", "timeDate", "tinytex", "urca", "utf8", "vctrs", "viridis", "viridisLite", "withr", "xfun", "yaml", "zoo" ], "_vignettes": [ { "source": "Introduction.Rmd", "filename": "Introduction.html", "title": "Introduction to phoenics", "author": "Camille Guilmineau, Rémi Servien et Nathalie Vialaneix", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "MTBLS422 dataset", "phoenics test", "Perform test", "Access test results", "Explore PCA results", "Options of phoenics main test function", "Switching from PCA to MFA", "Wrapper to automatically query pathways", "References", "Session information" ], "created": "2025-01-29 14:20:06", "modified": "2025-08-19 08:40:08", "commits": 2 } ], "_score": 2, "_indexed": true, "_nocasepkg": "phoenics", "_universes": [ "r-serv" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.6", "date": "2026-05-16T08:44:36.000Z", "distro": "noble", "commit": "d2537f0f96478d5f961848606ccc0ef01aa8b4c8", "fileid": "8db6e1d079eb17be25272646a6855edef41025a42b5d0720728885baa84b99ec", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/r-serv/actions/runs/25957510094" }, { "r": "4.6.0", "os": "linux", "version": "0.6", "date": "2026-05-16T08:44:26.000Z", "distro": "noble", "commit": "d2537f0f96478d5f961848606ccc0ef01aa8b4c8", "fileid": "f58ccacde4d9ff346290cc6fb163e2003daaeee05f9a61ea8af1529c6df0ed93", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/r-serv/actions/runs/25957510094" }, { "r": "4.5.3", "os": "mac", "version": "0.6", "date": "2026-05-16T08:44:08.000Z", "commit": "d2537f0f96478d5f961848606ccc0ef01aa8b4c8", "fileid": "48d7a0c5d616531350ea080ac7e0ae5ebc6fd14bdb86e5cb8dea5769745346b6", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/r-serv/actions/runs/25957510094" }, { "r": "4.6.0", "os": "mac", "version": "0.6", "date": "2026-05-16T08:43:53.000Z", "commit": "d2537f0f96478d5f961848606ccc0ef01aa8b4c8", "fileid": "40e79a68b5b1e7a0a14c4c44168b0f1ddc037cdd485abda4e30c1c3a1b82cca0", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/r-serv/actions/runs/25957510094" }, { "r": "4.7.0", "os": "win", "version": "0.6", "date": "2026-05-16T08:43:16.000Z", "commit": "d2537f0f96478d5f961848606ccc0ef01aa8b4c8", "fileid": "3be72639c7acc2f8e8654ad82713ef1c60082afa8d6947e107ba94c455c763e0", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/r-serv/actions/runs/25957510094" }, { "r": "4.5.3", "os": "win", "version": "0.6", "date": "2026-05-16T08:43:25.000Z", "commit": "d2537f0f96478d5f961848606ccc0ef01aa8b4c8", "fileid": "eac06a68106766fe6a376f5b822b8ab256fae659910b9a2e170998ee23fab264", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/r-serv/actions/runs/25957510094" }, { "r": "4.6.0", "os": "win", "version": "0.6", "date": "2026-05-16T08:43:12.000Z", "commit": "d2537f0f96478d5f961848606ccc0ef01aa8b4c8", "fileid": "446d071a653b2e6a349042027a1442885ba84701b3949bded933e108de2e87c9", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/r-serv/actions/runs/25957510094" }, { "r": "4.6.0", "os": "wasm", "version": "0.6", "date": "2026-06-02T18:13:21.000Z", "commit": "d2537f0f96478d5f961848606ccc0ef01aa8b4c8", "fileid": "1564005d0f74f30f491b45488d26f8b9e23393bd25390d3dd5ac9989ea7280ea", "status": "success", "buildurl": "https://github.com/r-universe/r-serv/actions/runs/25957510094" } ] }