Package: woven
Title: Weighted Omics View Embedding via Nystrom for Incomplete
        Multi-Omics Data
Version: 0.99.0
Authors@R: c(
    person("Nathan", "Bresette",
           role = c("aut", "cre"),
           email = "nathanbresette04@gmail.com",
           comment = c(ORCID = "0009-0003-1554-6006")),
    person("Ai-Ling", "Lin",
           role = "aut"),
    person("Jianlin", "Cheng",
           role = "aut"),
    person("National Institutes of Health / National Institute on Aging",
           role = "fnd",
           comment = "R56AG079586")
  )
Description: Supervised multi-omics integration for block-missing
        ("ragged") data. WOVEN learns a shared latent space across V
        omics modalities using only fully-observed anchor subjects,
        then projects block-missing subjects via Nystrom extension
        without feature-level imputation. Supervision via
        label-augmented cross-covariance (analogous to DIABLO) with
        optional sparse projection matrices (PMD). Designed for
        comparative effectiveness research where intersection-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,
        GeneExpression, Transcriptomics, Proteomics, Metabolomics,
        DimensionReduction, Clustering, Classification, Sequencing
Depends: R (>= 4.5.0)
Imports: Matrix, MatrixGenerics, RANN, cluster, parallel, stats
Suggests: ggplot2, RSpectra, testthat (>= 3.0.0), knitr, rmarkdown
VignetteBuilder: knitr
Config/testthat/edition: 3
Author: Nathan Bresette [aut, cre]
        (<https://orcid.org/0009-0003-1554-6006>), Ai-Ling Lin [aut],
        Jianlin Cheng [aut]
Maintainer: Nathan Bresette <nathanbresette04@gmail.com>
Repository: https://biocstaging.r-universe.dev
Date/Publication: 2026-06-24 19:26:06 UTC
RemoteUrl: https://github.com/BiocStaging/woven
RemoteRef: HEAD
RemoteSha: 3a4f0cc5ab3070cb30eb20dd1ca2efc82553bef0
NeedsCompilation: no
Packaged: 2026-06-24 20:36:43 UTC; root