Package: CLAMP
Type: Package
Title: Curated Latent-variable Analysis with Molecular Priors
Version: 0.99.3
Authors@R: 
    c(
      person("Marc", "Subirana-Granes", role = c("aut","cre"),
             email = "mb2subi@gmail.com",
             comment = c(ORCID = "0000-0003-3934-839X")),
      person("Maria", "Chikina", role = "aut",
             email = "mchikina@gmail.com"),
      person("National Human Genome Research Institute", role = "fnd",
             comment = "R00 HG011898 to M.P.; R01 HG009299-6A1 to M.C."),
      person("Eunice Kennedy Shriver National Institute of Child Health and Human Development",
             role = "fnd",
             comment = "R01 HD109765 to M.P."),
      person("National Science Foundation", role = "fnd",
             comment = "NSF 2238125 to M.C."),
      person("National Eye Institute", role = "fnd",
             comment = "NIH R01 EY030546-01A1 to M.C.")
    )
Description: CLAMP performs prior-informed latent variable decomposition of
    high-dimensional transcriptomic data. It integrates curated gene sets to
    learn biologically interpretable latent variables, supports file-backed
    matrices for large datasets, and provides tools for preprocessing,
    normalization, projection, and evaluation of latent structures. CLAMP is
    designed to scale to tens of thousands of samples, making it suitable for
    large public resources such as recount3 and ARCHS4. It enables researchers
    to uncover biologically meaningful patterns that connect genes, pathways,
    and complex traits in transcriptomics studies.
License: GPL-3
URL: https://chikinalab.github.io/CLAMP/,
        https://github.com/chikinalab/CLAMP
BugReports: https://github.com/chikinalab/CLAMP/issues
Depends: R (>= 4.6.0),
Imports: bigstatsr, circlize, ComplexHeatmap, dplyr, ggplot2, ggrepel,
        glmnet, grid, irlba, Matrix, matrixStats, methods, patchwork,
        Rcpp, rlang, rsvd, stats, utils
Suggests: AnnotationDbi, BiocStyle, CLAMPData, data.table, DiagrammeR,
        DT, rhdf5, here, knitr, org.Hs.eg.db, PCAtools, magick,
        rmarkdown, testthat (>= 3.0.0)
LinkingTo: Rcpp, RcppArmadillo
VignetteBuilder: knitr
biocViews: Software, GeneExpression, RNASeq, Transcriptomics,
        DimensionReduction, Visualization, Normalization, Pathways,
        Preprocessing, GenePrediction, GeneTarget
Encoding: UTF-8
LazyData: false
Roxygen: list(markdown = TRUE)
Config/testthat/edition: 3
Config/roxygen2/version: 8.0.0
RoxygenNote: 7.3.3
git_url: https://git.bioconductor.org/packages/CLAMP
git_branch: devel
git_last_commit: 1768d3b
git_last_commit_date: 2026-06-08
Repository: Bioconductor 3.24
Date/Publication: 2026-07-09
NeedsCompilation: yes
Packaged: 2026-07-09 20:59:49 UTC; biocbuild
Author: Marc Subirana-Granes [aut, cre] (ORCID:
    <https://orcid.org/0000-0003-3934-839X>),
  Maria Chikina [aut],
  National Human Genome Research Institute [fnd] (R00 HG011898 to M.P.;
    R01 HG009299-6A1 to M.C.),
  Eunice Kennedy Shriver National Institute of Child Health and Human
    Development [fnd] (R01 HD109765 to M.P.),
  National Science Foundation [fnd] (NSF 2238125 to M.C.),
  National Eye Institute [fnd] (NIH R01 EY030546-01A1 to M.C.)
Maintainer: Marc Subirana-Granes <mb2subi@gmail.com>
Built: R 4.6.1; x86_64-apple-darwin20; 2026-07-10 05:39:10 UTC; unix
