{ "_id": "6a1ac10c1d7bb097a09d765a", "Package": "padma", "Type": "Package", "Title": "Individualized Multi-Omic Pathway Deviation Scores Using\nMultiple Factor Analysis", "Version": "1.23.0", "Authors@R": "c(\nperson(given=\"Andrea\",\nfamily=\"Rau\",\nemail=\"andrea.rau@inrae.fr\",\nrole=c(\"cre\", \"aut\"),\ncomment = c(ORCID = \"0000-0001-6469-488X\")),\nperson(given=\"Regina\",\nfamily=\"Manansala\",\nemail=\"manansa2@uwm.edu\",\nrole=\"aut\"),\nperson(given=\"Florence\",\nfamily=\"Jaffrézic\",\nemail=\"florence.jaffrezic@inrae.fr\",\nrole=\"ctb\"),\nperson(given=\"Denis\",\nfamily=\"Laloë\",\nemail=\"denis.laloe@inrae.fr\",\nrole=\"aut\"),\nperson(given=\"Paul\",\nfamily=\"Auer\",\nemail=\"pauer@uwm.edu\",\nrole=\"aut\"))", "Description": "Use multiple factor analysis to calculate individualized\npathway-centric scores of deviation with respect to the sampled\npopulation based on multi-omic assays (e.g., RNA-seq, copy\nnumber alterations, methylation, etc). Graphical and numerical\noutputs are provided to identify highly aberrant individuals\nfor a particular pathway of interest, as well as the gene and\nomics drivers of aberrant multi-omic profiles.", "License": "GPL (>=3)", "URL": "https://github.com/andreamrau/padma", "https": "//github.com/andreamrau/padma/issues", "biocViews": "Software, StatisticalMethod, PrincipalComponent,\nGeneExpression, Pathways, RNASeq, BioCarta, MethylSeq", "Encoding": "UTF-8", "LazyData": "TRUE", "RoxygenNote": "7.3.1", "VignetteBuilder": "knitr", "Config/pak/sysreqs": "cmake make libicu-dev libuv1-dev zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:53:06 UTC", "RemoteUrl": "https://github.com/bioc/padma", "RemoteRef": "HEAD", "RemoteSha": "836ee71cb5f88bbd4c6f931754648e0d889a2099", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-30 07:19:24 UTC", "User": "root" }, "Author": "Andrea Rau [cre, aut] (ORCID: ),\nRegina Manansala [aut],\nFlorence Jaffrézic [ctb],\nDenis Laloë [aut],\nPaul Auer [aut]", "Maintainer": "Andrea Rau ", "MD5sum": "471b0af9a2c68509d223f2ebf8235c9e", "_user": "bioc", "_type": "src", "_file": "padma_1.23.0.tar.gz", "_fileid": "583d0d23191c19e75afb639e87862a59dd87f398772274677e5abf3c8b69040b", "_filesize": 1281791, "_sha256": "583d0d23191c19e75afb639e87862a59dd87f398772274677e5abf3c8b69040b", "_created": "2026-05-30T07:19:24.000Z", "_published": "2026-05-30T10:50:52.465Z", "_jobs": [ { "job": 78633058553, "time": 205, "config": "bioc-checks", "r": "4.6.0", "check": "NOTE", "artifact": "7306434567" }, { "job": 78633058565, "time": 348, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7306449807" }, { "job": 78633058570, "time": 315, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7306445988" }, { "job": 78633058561, "time": 243, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7307551606" }, { "job": 78633058560, "time": 252, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7307550763" }, { "job": 78632826517, "time": 264, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7306412206" }, { "job": 78633058558, "time": 174, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7306431223" }, { "job": 78633058618, "time": 236, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7306437758" }, { "job": 78633058621, "time": 250, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7306439176" }, { "job": 78633058579, "time": 267, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7306441032" } ], "_bioccheck": { "error": 0, "warning": 0, "note": 13 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26677817819", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/padma", "_commit": { "id": "836ee71cb5f88bbd4c6f931754648e0d889a2099", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777380786 }, "_maintainer": { "name": "Andrea Rau", "email": "andrea.rau@inrae.fr", "login": "andreamrau", "twitter": "@andreamrau", "description": "\n Research scientist in statistics + genomics\n", "uuid": 12795415, "orcid": "0000-0001-6469-488X" }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.1.0", "role": "Depends" }, { "package": "SummarizedExperiment", "role": "Depends" }, { "package": "S4Vectors", "role": "Depends" }, { "package": "FactoMineR", "role": "Imports" }, { "package": "MultiAssayExperiment", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "graphics", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "testthat", "role": "Suggests" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "KEGGREST", "role": "Suggests" }, { "package": "missMDA", "role": "Suggests" }, { "package": "ggplot2", "role": "Suggests" }, { "package": "ggrepel", "role": "Suggests" }, { "package": "car", "role": "Suggests" }, { "package": "cowplot", "role": "Suggests" }, { "package": "reshape2", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.23.0", "bioc": "3.24" }, { "branch": "release", "version": "1.22.0", "bioc": "3.23" } ], "_topics": [ "software", "statisticalmethod", "principalcomponent", "geneexpression", "pathways", "rnaseq", "biocarta", "methylseq" ], "_stars": 3, "_contributors": [ { "user": "andreamrau", "count": 39, "uuid": 12795415 }, { "user": "nturaga", "count": 8, "uuid": 2746443 }, { "user": "jwokaty", "count": 8, "uuid": 1744257 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 382, "source": "https://www.bioconductor.org/packages/stats/bioc/padma" }, "_devurl": "https://github.com/andreamrau/padma", "_searchresults": 6, "_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/padma.html", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/andreamrau/padma", "_realowner": "bioc", "_cranurl": false, "_exports": [ "factorMap", "imputed_genes", "MFA_results", "ngenes", "omicsContrib", "padma", "padmaRun", "pathway_gene_deviation", "pathway_name", "removed_genes", "show" ], "_datasets": [ { "name": "LUAD_subset", "title": "Subset of batch-corrected multi-omic TCGA data in lung adenocarcinoma", "object": "LUAD_subset", "class": [ "list" ], "fields": [], "table": false, "tojson": true }, { "name": "mirtarbase", "title": "Curated miR-target interaction predictions from miRTarBase", "object": "mirtarbase", "class": [ "data.frame" ], "fields": [ "miRNA", "Target Gene" ], "rows": 10754, "table": true, "tojson": true }, { "name": "msigdb", "title": "MSigDB canonical pathways and corresponding gene lists", "object": "msigdb", "class": [ "data.frame" ], "fields": [ "geneset", "symbol" ], "rows": 1322, "table": true, "tojson": true } ], "_help": [ { "page": "factorMap", "title": "Plot an MFA factor map for individuals or partial factor map based on padma analysis", "topics": [ "factorMap" ] }, { "page": "LUAD_subset", "title": "Subset of batch-corrected multi-omic TCGA data in lung adenocarcinoma", "topics": [ "LUAD_subset" ] }, { "page": "mirtarbase", "title": "Curated miR-target interaction predictions from miRTarBase", "topics": [ "mirtarbase" ] }, { "page": "msigdb", "title": "MSigDB canonical pathways and corresponding gene lists", "topics": [ "msigdb" ] }, { "page": "omicsContrib", "title": "Plot the omics contribution per MFA axis and the overall weighted contribution", "topics": [ "omicsContrib" ] }, { "page": "padma", "title": "Calculate individualized deviation scores from multi-omic data", "topics": [ "padma", "padma,list-method", "padma,MultiAssayExperiment-method", "padma-methods" ] }, { "page": "padmaResults", "title": "padmaResults object and constructor", "topics": [ "padmaResults", "padmaResults-class" ] }, { "page": "padmaRun", "title": "Calculate individualized deviation scores from multi-omic data", "topics": [ "padmaRun" ] }, { "page": "padmaHelpers", "title": "Accessors for a padmaResults object.", "topics": [ "imputed_genes", "imputed_genes,padmaResults-method", "MFA_results", "MFA_results,padmaResults-method", "ngenes", "ngenes,padmaResults-method", "pathway_gene_deviation", "pathway_gene_deviation,padmaResults-method", "pathway_gene_deviation-method", "pathway_name", "pathway_name,padmaResults-method", "removed_genes", "removed_genes,padmaResults-method", "show", "show,padmaResults-method" ] }, { "page": "summary", "title": "Summarize results from padma", "topics": [ "summary", "summary,padmaResults-method", "summary-methods" ] } ], "_readme": "https://github.com/bioc/padma/raw/HEAD/README.md", "_rundeps": [ "abind", "backports", "base64enc", "Biobase", "BiocBaseUtils", "BiocGenerics", "boot", "broom", "bslib", "cachem", "car", "carData", "cli", "cluster", "colorspace", "cowplot", "cpp11", "crosstalk", "DelayedArray", "Deriv", "digest", "doBy", "dplyr", "DT", "ellipse", "emmeans", "estimability", "evaluate", "FactoMineR", "farver", "fastmap", "flashClust", "fontawesome", "forecast", "Formula", "fracdiff", "fs", "generics", "GenomicRanges", "ggplot2", "ggrepel", "glue", "gtable", "highr", "htmltools", "htmlwidgets", "IRanges", "isoband", "jquerylib", "jsonlite", "knitr", "labeling", "later", "lattice", "lazyeval", "leaps", "lifecycle", "lme4", "lmtest", "magrittr", "MASS", "Matrix", "MatrixGenerics", "MatrixModels", "matrixStats", "memoise", "mgcv", "microbenchmark", "mime", "minqa", "modelr", "multcompView", "MultiAssayExperiment", "mvtnorm", "nlme", "nloptr", "nnet", "numDeriv", "otel", "pbkrtest", "pillar", "pkgconfig", "promises", "purrr", "quantreg", "R6", "rappdirs", "rbibutils", "RColorBrewer", "Rcpp", "RcppArmadillo", "RcppEigen", "Rdpack", "reformulas", "rlang", "rmarkdown", "S4Arrays", "S4Vectors", "S7", "sass", "scales", "scatterplot3d", "Seqinfo", "SparseArray", "SparseM", "stringi", "stringr", "SummarizedExperiment", "survival", "tibble", "tidyr", "tidyselect", "timeDate", "tinytex", "urca", "utf8", "vctrs", "viridisLite", "withr", "xfun", "XVector", "yaml", "zoo" ], "_vignettes": [ { "source": "padma.Rmd", "filename": "padma.html", "title": "padma package: Quick-start guide", "author": "Andrea Rau", "engine": "knitr::rmarkdown", "headings": [ "Quick start (tl;dr)", "Description of padma", "Overview of Multiple Factor Analysis", "Calculation of individualized pathway deviation scores", "Calculation of individualized per-gene deviation scores", "Description of built-in datasets", "LUAD_subset: D4-GDI signaling pathway in the TCGA-LUAD multi-omic data", "msigdb: the MSigDB canonical pathway gene sets", "mirtarbase: predicted gene targets of miRNAs", "Running padma", "Numerical outputs", "Graphical outputs", "Additional options", "Projecting supplementary individuals onto a reference consensus", "Missing data imputation", "Providing miRNA target predictions", "Requesting concise results from padma", "FAQ", "To-do list and ideas for work in progress", "Session Info" ], "created": "2020-01-09 13:39:09", "modified": "2021-10-14 14:04:53", "commits": 3 } ], "_score": 4.778151250383644, "_indexed": true, "_nocasepkg": "padma", "_universes": [ "bioc", "andreamrau" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.23.0", "date": "2026-05-30T07:23:07.000Z", "distro": "noble", "commit": "836ee71cb5f88bbd4c6f931754648e0d889a2099", "fileid": "a986ce2ccd4cf76dcc5d79591760885623dcb745edc45b3e35f2b7b1c9baaef8", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677817819" }, { "r": "4.6.0", "os": "linux", "version": "1.23.0", "date": "2026-05-30T07:22:51.000Z", "distro": "noble", "commit": "836ee71cb5f88bbd4c6f931754648e0d889a2099", "fileid": "1ed24c39310b524e67fd470060817afffbd39d099256ce9e6618240660ccb367", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677817819" }, { "r": "4.5.3", "os": "mac", "version": "1.23.0", "date": "2026-05-30T10:33:17.000Z", "commit": "836ee71cb5f88bbd4c6f931754648e0d889a2099", "fileid": "d48e2f6d2e46a21506c3af875b1d692343e5d3f1fe63ae91081ac842df87331e", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677817819" }, { "r": "4.6.0", "os": "mac", "version": "1.23.0", "date": "2026-05-30T10:32:43.000Z", "commit": "836ee71cb5f88bbd4c6f931754648e0d889a2099", "fileid": "ff89350856c66a8890a1b76d1e3872543327f1bd078f69155041d399879ef9ee", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677817819" }, { "r": "4.6.0", "os": "wasm", "version": "1.23.0", "date": "2026-05-30T07:22:51.000Z", "commit": "836ee71cb5f88bbd4c6f931754648e0d889a2099", "fileid": "47c89c1fcfb31daee0a7a4c9504f16f8c6b29eec10e99a6aa055cb171f12f2b8", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677817819" }, { "r": "4.7.0", "os": "win", "version": "1.23.0", "date": "2026-05-30T07:21:18.000Z", "commit": "836ee71cb5f88bbd4c6f931754648e0d889a2099", "fileid": "4e8a69acd47e5998607489fbb61b3bacbde9312db77e7fac598c81868e12a76b", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677817819" }, { "r": "4.5.3", "os": "win", "version": "1.23.0", "date": "2026-05-30T07:21:24.000Z", "commit": "836ee71cb5f88bbd4c6f931754648e0d889a2099", "fileid": "de10374c1bd3fc7a07a3884570cf3649a4a8ce2206cb5487475346da3fc1b3b7", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677817819" }, { "r": "4.6.0", "os": "win", "version": "1.23.0", "date": "2026-05-30T07:21:44.000Z", "commit": "836ee71cb5f88bbd4c6f931754648e0d889a2099", "fileid": "bdf604b3c94e0133ff58b0a98308b9243f8d87add24ac0eb4b39d4ab7a473ae0", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677817819" } ] }