{ "_id": "6aad96da3d719c1f8407791b", "Package": "woven", "Title": "Weighted Omics View Embedding via Nystrom for Incomplete\nMulti-Omics Data", "Version": "0.99.3", "Authors@R": "c(\nperson(\"Nathan\", \"Bresette\",\nrole = c(\"aut\", \"cre\"),\nemail = \"nathanbresette04@gmail.com\",\ncomment = c(ORCID = \"0009-0003-1554-6006\")),\nperson(\"Ai-Ling\", \"Lin\",\nrole = \"aut\"),\nperson(\"Jianlin\", \"Cheng\",\nrole = \"aut\"),\nperson(\"National Institutes of Health / National Institute on Aging\",\nrole = \"fnd\",\ncomment = \"R56AG079586\")\n)", "Description": "Supervised multi-omics integration for block-missing\n(\"ragged\") data. WOVEN learns a shared latent space across V\nomics modalities using only fully-observed anchor subjects,\nthen projects block-missing subjects via Nystrom extension\nwithout feature-level imputation. Supervision enters through a\nlabel-augmented cross-covariance (analogous to DIABLO), and\nprojection matrices can optionally be ridge-regularized and\nunivariately feature-screened for high-dimensional modalities.\nDesigned for comparative effectiveness research where\nintersection-only methods introduce selection bias.", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "RoxygenNote": "7.3.3", "URL": "https://github.com/NathanBresette/woven", "BugReports": "https://github.com/NathanBresette/woven/issues", "biocViews": "Software, StatisticalMethod, MultipleComparison,\nGeneExpression, Transcriptomics, Proteomics, Metabolomics,\nDimensionReduction, Clustering, Classification, Sequencing", "VignetteBuilder": "knitr", "Config/testthat/edition": "3", "Author": "Nathan Bresette [aut, cre]\n(), Ai-Ling Lin [aut],\nJianlin Cheng [aut]", "Maintainer": "Nathan Bresette ", "Repository": "https://biocstaging.r-universe.dev", "Date/Publication": "2026-09-18 19:02:00 UTC", "RemoteUrl": "https://github.com/BiocStaging/woven", "RemoteRef": "HEAD", "RemoteSha": "5f9ecfb94bc2ecf16a1ebd2810facc3d748b13ea", "NeedsCompilation": "no", "Packaged": { "Date": "2026-09-18 19:50:03 UTC", "User": "root" }, "_user": "biocstaging", "_type": "src", "_file": "woven_0.99.3.tar.gz", "_fileid": "https://r2.ropensci.org/6637e6c03f342de866bbe54885c267adc27a30aebbec25fc9f3630dde1d9be36", "_filesize": 683774, "_sha256": "6637e6c03f342de866bbe54885c267adc27a30aebbec25fc9f3630dde1d9be36", "_expires": "2026-12-27T19:53:59.000Z", "_created": "2026-09-18T19:50:03.000Z", "_published": "2026-09-18T19:54:01.885Z", "_bioccheck": { "error": 0, "warning": 0, "note": 3 }, "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/biocstaging/actions/runs/35387809969", "_status": "success", "_upstream": "https://github.com/BiocStaging/woven", "_commit": { "id": "5f9ecfb94bc2ecf16a1ebd2810facc3d748b13ea", "author": "Nathan Bresette ", "committer": "Nathan Bresette ", "message": "woven 0.99.3: bump version for BiocCheck-fix commit (reviewer requested)\n\nb24c498 shipped real fixes (stray check-output dir in tarball, stale\nDESCRIPTION claim, BiocCheck NOTEs, new tests) without a version bump,\nso R-universe never generated a new build report. vjcitn flagged this\non the Bioconductor review thread and asked for a version bump.\n\nCo-Authored-By: Claude Sonnet 5 \nClaude-Session: https://claude.ai/code/session_01SzktWVDr7KCpUFXaWBduoH\n", "time": 1789758120 }, "_maintainer": { "name": "Nathan Bresette", "email": "nathanbresette04@gmail.com", "login": "nathanbresette", "description": "", "uuid": 148147840, "orcid": "0009-0003-1554-6006" }, "_distro": "resolute", "_jobs": [ { "job": 105739896885, "time": 193, "config": "bioc-checks", "r": "4.6.1", "check": "NOTE", "artifact": "10564782921" }, { "job": 105739896940, "time": 195, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "10564314295" }, { "job": 105739896864, "time": 191, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "10564458569" }, { "job": 105739896948, "time": 102, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "10564797641" }, { "job": 105739896919, "time": 134, "config": "macos-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "10564637912" }, { "job": 105738821048, "time": 207, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "10564243922" }, { "job": 105739896929, "time": 165, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "10564393941" }, { "job": 105739896989, "time": 144, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "10564857686" }, { "job": 105739896920, "time": 145, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "10564259229" }, { "job": 105739896993, "time": 122, "config": "windows-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "10564757696" } ], "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.5.0", "role": "Depends" }, { "package": "Matrix", "role": "Imports" }, { "package": "MatrixGenerics", "role": "Imports" }, { "package": "RANN", "role": "Imports" }, { "package": "cluster", "role": "Imports" }, { "package": "parallel", "role": "Imports" }, { "package": "BiocParallel", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "ggplot2", "role": "Suggests" }, { "package": "RSpectra", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "MultiAssayExperiment", "role": "Suggests" }, { "package": "SummarizedExperiment", "role": "Suggests" } ], "_owner": "biocstaging", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2026-25", "n": 11 }, { "week": "2026-26", "n": 10 }, { "week": "2026-28", "n": 2 }, { "week": "2026-36", "n": 2 }, { "week": "2026-38", "n": 3 } ], "_tags": [], "_topics": [ "software", "statisticalmethod", "multiplecomparison", "geneexpression", "transcriptomics", "proteomics", "metabolomics", "dimensionreduction", "clustering", "classification", "sequencing" ], "_stars": 0, "_contributors": [ { "user": "nathanbresette", "count": 28, "uuid": 148147840 } ], "_userbio": { "uuid": 278472782, "type": "organization", "name": "BiocStaging", "followers": 2 }, "_downloads": { "count": 0, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/woven" }, "_devurl": "https://github.com/nathanbresette/woven", "_searchresults": 3, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/manual.pdf", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "extra/woven.html", "LICENSE" ], "_cranurl": false, "_exports": [ "anchorIdx", "plot", "show", "singularValues", "summary", "WList", "woven", "woven_davies_bouldin", "woven_effect_bias", "woven_ess_retention", "woven_mcca_dual", "woven_metrics", "woven_nmi", "woven_nystrom_error", "woven_plot_loadings", "woven_plot_variance", "woven_plot_vip", "woven_precompute", "woven_predict", "woven_rv", "woven_scores", "woven_silhouette", "Z" ], "_datasets": [ { "name": "woven_example", "title": "Example dataset for WOVEN", "object": "woven_example", "file": "woven_example.rda", "class": [ "list" ], "fields": [], "table": false, "tojson": true } ], "_help": [ { "page": "anchorIdx", "title": "Indices of the anchor (fully-observed) subjects", "topics": [ "anchorIdx", "anchorIdx,woven-method" ] }, { "page": "plot-woven-missing-method", "title": "Plot the WOVEN latent space", "topics": [ "plot,woven,missing-method" ] }, { "page": "show-woven-method", "title": "Show method for WOVEN fit", "topics": [ "show,woven-method" ] }, { "page": "singularValues", "title": "Supervised canonical correlations", "topics": [ "singularValues", "singularValues,woven-method" ] }, { "page": "summary-woven-method", "title": "Summarise a WOVEN fit", "topics": [ "summary,woven-method" ] }, { "page": "WList", "title": "Per-modality projection matrices", "topics": [ "WList", "WList,woven-method" ] }, { "page": "woven", "title": "Fit a supervised WOVEN model", "topics": [ "woven" ] }, { "page": "woven_davies_bouldin", "title": "Davies-Bouldin index", "topics": [ "woven_davies_bouldin" ] }, { "page": "woven_effect_bias", "title": "CER-specific: subgroup effect estimate bias", "topics": [ "woven_effect_bias" ] }, { "page": "woven_ess_retention", "title": "Effective sample size retention", "topics": [ "woven_ess_retention" ] }, { "page": "woven_example", "title": "Example dataset for WOVEN", "topics": [ "woven_example" ] }, { "page": "woven_mcca_dual", "title": "Fit supervised WOVEN for V >= 2 views via dual SUMCOR MCCA (closed-form)", "topics": [ "woven_mcca_dual" ] }, { "page": "woven_metrics", "title": "Convenience wrapper: compute core metrics directly from a woven fit", "topics": [ "woven_metrics" ] }, { "page": "woven_nmi", "title": "Normalized mutual information between cluster assignments and true labels", "topics": [ "woven_nmi" ] }, { "page": "woven_nystrom_error", "title": "Leave-anchor-out Nystrom projection error", "topics": [ "woven_nystrom_error" ] }, { "page": "woven_plot_loadings", "title": "Plot feature loadings for one WOVEN latent dimension", "topics": [ "woven_plot_loadings" ] }, { "page": "woven_plot_variance", "title": "Plot variance explained per WOVEN latent dimension", "topics": [ "woven_plot_variance" ] }, { "page": "woven_plot_vip", "title": "Plot VIP scores for a WOVEN modality", "topics": [ "woven_plot_vip" ] }, { "page": "woven_precompute", "title": "Pre-compute Laplacian graphs for reuse across multiple woven() calls", "topics": [ "woven_precompute" ] }, { "page": "woven_predict", "title": "Predict class probabilities for new subjects", "topics": [ "woven_predict" ] }, { "page": "woven_rv", "title": "RV coefficient between latent scores and ground-truth factor matrix", "topics": [ "woven_rv" ] }, { "page": "woven_scores", "title": "Extract latent scores for new subjects", "topics": [ "woven_scores" ] }, { "page": "woven_silhouette", "title": "Average silhouette width", "topics": [ "woven_silhouette" ] }, { "page": "woven-class", "title": "S4 class for a fitted WOVEN model", "topics": [ "woven-class" ] }, { "page": "Z", "title": "Consensus latent scores", "topics": [ "Z", "Z,woven-method" ] } ], "_readme": "https://github.com/BiocStaging/woven/raw/HEAD/README.md", "_rundeps": [ "BH", "BiocParallel", "cluster", "codetools", "cpp11", "formatR", "futile.logger", "futile.options", "lambda.r", "lattice", "Matrix", "MatrixGenerics", "matrixStats", "RANN", "snow" ], "_vignettes": [ { "source": "woven-intro.Rmd", "filename": "woven-intro.html", "title": "Introduction to WOVEN: Multi-Omics Integration for Incomplete Patient Data", "author": "Nathan Bresette, Ai-Ling Lin, Jianlin Cheng", "engine": "knitr::rmarkdown", "headings": [ "Overview", "Installation", "Preparing Your Data", "Input format", "Pre-processing recommendations", "Quick Start", "Simulate a three-modality dataset", "Induce block-level missingness", "Fit WOVEN", "Exploring Results", "Latent space scatter", "VIP scores: which features matter most?", "Feature loadings: direction of effect", "Variance explained: choosing K", "Quantitative metrics", "Predicting New Subjects", "Comparing WOVEN and DIABLO: Effective Sample Size", "Accessing Raw Results", "Session Info" ], "created": "2026-06-16 13:50:42", "modified": "2026-09-17 21:23:33", "commits": 7 } ], "_score": 3.3979400086720375, "_indexed": true, "_nocasepkg": "woven", "_universes": [ "biocstaging", "nathanbresette" ], "_previous": "0.99.2", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.99.3", "date": "2026-09-18T19:52:42.000Z", "distro": "resolute", "commit": "5f9ecfb94bc2ecf16a1ebd2810facc3d748b13ea", "fileid": "https://r2.ropensci.org/78243980e60a8b748fa2b46da50e1eb81d8b12d544b41afd7087ee3d391a54a6", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/biocstaging/actions/runs/35387809969" }, { "r": "4.6.1", "os": "linux", "version": "0.99.3", "date": "2026-09-18T19:52:40.000Z", "distro": "resolute", "commit": "5f9ecfb94bc2ecf16a1ebd2810facc3d748b13ea", "fileid": "https://r2.ropensci.org/816084843871fda0900627eb4709395e618313ecb3ce5f579677be4e189160eb", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/biocstaging/actions/runs/35387809969" }, { "r": "4.5.3", "os": "mac", "version": "0.99.3", "date": "2026-09-18T19:51:35.000Z", "commit": "5f9ecfb94bc2ecf16a1ebd2810facc3d748b13ea", "fileid": "https://r2.ropensci.org/82039ea29d89470afa4fee1c86b06ab8ffd1db0e629a7fa758182aced5915e90", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/biocstaging/actions/runs/35387809969" }, { "r": "4.6.1", "os": "mac", "version": "0.99.3", "date": "2026-09-18T19:51:58.000Z", "commit": "5f9ecfb94bc2ecf16a1ebd2810facc3d748b13ea", "fileid": "https://r2.ropensci.org/7d48b62aa4be4edc660b3accf6eac7b3069a787cfc154ef442578251fd188fd6", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/biocstaging/actions/runs/35387809969" }, { "r": "4.6.0", "os": "wasm", "version": "0.99.3", "date": "2026-09-18T19:53:07.000Z", "commit": "5f9ecfb94bc2ecf16a1ebd2810facc3d748b13ea", "fileid": "https://r2.ropensci.org/de006d49aa69c6b16990aad444e412aff742cf64b245a8509ba520b87e11b162", "status": "success", "buildurl": "https://github.com/r-universe/biocstaging/actions/runs/35387809969" }, { "r": "4.7.0", "os": "win", "version": "0.99.3", "date": "2026-09-18T19:51:47.000Z", "commit": "5f9ecfb94bc2ecf16a1ebd2810facc3d748b13ea", "fileid": "https://r2.ropensci.org/00b79549ea566fb92d2be5675d1e920fefc434557b7881467a7036a87fdc31ad", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/biocstaging/actions/runs/35387809969" }, { "r": "4.5.3", "os": "win", "version": "0.99.3", "date": "2026-09-18T19:51:47.000Z", "commit": "5f9ecfb94bc2ecf16a1ebd2810facc3d748b13ea", "fileid": "https://r2.ropensci.org/dada4dda3877f6e440bb39dbb611bf3deca3b8661f2d58ec3c60d70680a62535", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/biocstaging/actions/runs/35387809969" }, { "r": "4.6.1", "os": "win", "version": "0.99.3", "date": "2026-09-18T19:51:28.000Z", "commit": "5f9ecfb94bc2ecf16a1ebd2810facc3d748b13ea", "fileid": "https://r2.ropensci.org/5eedd1f8cf70aec10d2d8d1a3463cc8ab5b14b804162d1af802e44946289df7b", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/biocstaging/actions/runs/35387809969" } ] }