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 (>= 4.5.0),
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
Config/pak/sysreqs: libpng-dev perl
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-06-08 15:36:17 UTC
RemoteUrl: https://github.com/bioc/CLAMP
RemoteRef: HEAD
RemoteSha: 1768d3b1bc1ed9f6c7029ca870f5b013c191aee0
NeedsCompilation: yes
Packaged: 2026-06-21 00:44:03 UTC; root
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>