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"title": "Retrieve the subnetwork membership for each feature", "topics": [ "subnetworkMembership", "subnetworkMembership,consensusClusteringResults-method", "subnetworkMembership,DNEA-method" ] }, { "page": "sumExp2DNEA", "title": "Initialize a DNEA from SummarizedExperiment", "topics": [ "sumExp2DNEA" ] }, { "page": "T1Dmeta", "title": "Sample meta data for the The Environmental Determinants of Diabetes in the Young (TEDDY) clinical trial", "topics": [ "T1Dmeta" ] }, { "page": "TEDDY", "title": "Example expresion data set from The Environmental Determinants of Diabetes in the Young (TEDDY) clinical trial", "topics": [ "TEDDY" ] } ], "_readme": "https://github.com/bioc/DNEA/raw/HEAD/README.md", "_rundeps": [ "abind", "annotate", "AnnotationDbi", "askpass", "assertthat", "babelgene", "backports", "base64enc", "base64url", "BH", "Biobase", "BiocGenerics", "BiocParallel", "Biostrings", "bit", "bit64", "bitops", "blob", "cachem", "caTools", "cli", "codetools", "corpcor", "cpp11", 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"utf8", "uuid", "vctrs", "withr", "XML", "xtable", "XVector" ], "_vignettes": [ { "source": "DNEA.Rmd", "filename": "DNEA.html", "title": "Differential Network Expression Analysis for Metabolomics Data", "author": "Christopher P. Patsalis", "engine": "knitr::rmarkdown", "headings": [ "Downloading DNEA", "Basic DNEA workflow", "Example Data", "Quick Start", "Input data", "expression_data", "group_labels", "STEP 1: Data pre-processing and feature aggregation", "Data pre-processing", "Feature Aggregation", "[OPTIONAL] Custom-Normalized Data Input", "STEP 2: Model Tuning", "$\\lambda$ tuning via BIC", "Stability Selection", "Step 3: Constructing the Networks and Consensus Clustering", "Constructing the Networks", "Consensus Clustering", "Step 4: Pathway Enrichment via NetGSA and Network Visualization", "Pathway Enrichment via NetGSA", "Network Visualization", "Citation", "Session info", "References" ], "created": "2023-08-23 21:41:24", "modified": "2025-04-23 19:52:07", "commits": 29 } ], "_score": 4.778151250383644, "_indexed": true, "_nocasepkg": "dnea", "_universes": [ "bioc", "chrispatsalis", "karnovsky-lab" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.3.0", "date": "2026-05-30T08:48:00.000Z", "distro": "noble", "commit": "3efd42f7cacf7e7e77aed34e9a57984cac6aac3b", "fileid": "f34a23b460a98828a7b436476352bd07c4ab4ef35cb875d3c1ebd1cefa543264", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679427070" }, { "r": "4.6.0", "os": "linux", "version": "1.3.0", "date": "2026-05-30T08:49:08.000Z", "distro": "noble", "commit": "3efd42f7cacf7e7e77aed34e9a57984cac6aac3b", "fileid": "c8dea74c2dbff5e1e4020a778f1dd09b027b6c6a141c488c282ea8f3d455f7ee", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679427070" }, { "r": "4.5.3", "os": "mac", "version": "1.3.0", "date": "2026-05-30T12:15:14.000Z", "commit": "3efd42f7cacf7e7e77aed34e9a57984cac6aac3b", "fileid": "4588936c4eedbb031dca1f4bbaf043e466c0069022a16c4df1b6c1045e392a3e", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679427070" }, { "r": "4.6.0", "os": "mac", "version": "1.3.0", "date": "2026-05-30T12:15:03.000Z", "commit": "3efd42f7cacf7e7e77aed34e9a57984cac6aac3b", "fileid": "d71d7a5ad94a85c33e0ca323696a3c69174cd650e26a04e6fdc0ccf4611de495", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679427070" }, { "r": "4.6.0", "os": "wasm", "version": "1.3.0", "date": "2026-05-30T08:48:27.000Z", "commit": "3efd42f7cacf7e7e77aed34e9a57984cac6aac3b", "fileid": "5731614dd7fbd977a27c634fae3945a51cc451b6d85f3cca97c476007167c4ba", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679427070" }, { "r": "4.7.0", "os": "win", "version": "1.3.0", "date": "2026-05-30T08:53:23.000Z", "commit": "3efd42f7cacf7e7e77aed34e9a57984cac6aac3b", "fileid": "ea7677692a7d048f0cc9a1d77718adafa65c5ee94f106979be33b72ae26eb8bb", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679427070" }, { "r": "4.5.3", "os": "win", "version": "1.3.0", "date": "2026-05-30T08:52:46.000Z", "commit": "3efd42f7cacf7e7e77aed34e9a57984cac6aac3b", "fileid": "2e0fab95038bf60dbcfc8d6bc4a2efbc780c9bef0a5c78a97b1b4fb1ada93837", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679427070" }, { "r": "4.6.0", "os": "win", "version": "1.3.0", "date": "2026-05-30T08:46:56.000Z", "commit": "3efd42f7cacf7e7e77aed34e9a57984cac6aac3b", "fileid": "98e7d11a66fdab7cf097fe10fd7b5c4358d1a5eedb49a9860aded3db1668f7ba", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679427070" } ] }