Package: scPCA
Title: Sparse Contrastive Principal Component Analysis
Version: 1.25.0
Authors@R: c(
    person(given = "Philippe",
           family = "Boileau",
           role = c("aut", "cre", "cph"),
           email = "philippe_boileau@berkeley.edu",
           comment = c(ORCID = "0000-0002-4850-2507")),
    person(given = "Nima",
           family = "Hejazi",
           role = "aut",
           email = "nh@nimahejazi.org",
           comment = c(ORCID = "0000-0002-7127-2789")),
    person(given = "Sandrine",
           family = "Dudoit",
           role = c("ctb", "ths"),
           email = "sandrine@stat.berkeley.edu",
           comment = c(ORCID = "0000-0002-6069-8629"))
   )
Description: A toolbox for sparse contrastive principal component
        analysis (scPCA) of high-dimensional biological data. scPCA
        combines the stability and interpretability of sparse PCA with
        contrastive PCA's ability to disentangle biological signal from
        unwanted variation through the use of control data. Also
        implements and extends cPCA.
Depends: R (>= 4.0.0)
Imports: stats, methods, assertthat, tibble, dplyr, purrr, stringr,
        Rdpack, matrixStats, BiocParallel, elasticnet, sparsepca,
        cluster, kernlab, origami, RSpectra, coop, Matrix,
        DelayedArray, ScaledMatrix, MatrixGenerics
Suggests: DelayedMatrixStats, sparseMatrixStats, testthat (>= 2.1.0),
        covr, knitr, rmarkdown, BiocStyle, ggplot2, ggpubr, splatter,
        SingleCellExperiment, microbenchmark
License: MIT + file LICENSE
URL: https://github.com/PhilBoileau/scPCA
BugReports: https://github.com/PhilBoileau/scPCA/issues
Encoding: UTF-8
LazyData: true
VignetteBuilder: knitr
RoxygenNote: 7.3.1
RdMacros: Rdpack
biocViews: PrincipalComponent, GeneExpression, DifferentialExpression,
        Sequencing, Microarray, RNASeq
Config/pak/sysreqs: libicu-dev zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2025-10-29 14:55:26 UTC
RemoteUrl: https://github.com/bioc/scPCA
RemoteRef: HEAD
RemoteSha: 93c5905624064e225ae9305f4f96ad2177d5d190
NeedsCompilation: no
Packaged: 2026-01-16 22:03:02 UTC; root
Author: Philippe Boileau [aut, cre, cph] (ORCID:
    <https://orcid.org/0000-0002-4850-2507>),
  Nima Hejazi [aut] (ORCID: <https://orcid.org/0000-0002-7127-2789>),
  Sandrine Dudoit [ctb, ths] (ORCID:
    <https://orcid.org/0000-0002-6069-8629>)
Maintainer: Philippe Boileau <philippe_boileau@berkeley.edu>
Built: R 4.6.0; ; 2026-01-16 22:05:40 UTC; unix
