Package: ReducedExperiment
Type: Package
Title: Containers and tools for dimensionally-reduced -omics
        representations
Version: 1.2.0
Authors@R: c(
    person("Jack", "Gisby", , "jackgisby@gmail.com", role = c("aut", "cre"),
           comment = c(ORCID = "0000-0003-0511-8123")),
    person("Michael", "Barnes", , "m.r.barnes@qmul.ac.uk", role = c("aut"),
           comment = c(ORCID = "0000-0001-9097-7381"))
    )
Date: 2024-07-30
Description: Provides SummarizedExperiment-like containers for storing
        and manipulating dimensionally-reduced assay data. The
        ReducedExperiment classes allow users to simultaneously
        manipulate their original dataset and their decomposed data, in
        addition to other method-specific outputs like feature
        loadings. Implements utilities and specialised classes for the
        application of stabilised independent component analysis (sICA)
        and weighted gene correlation network analysis (WGCNA).
License: GPL (>= 3)
Encoding: UTF-8
Depends: R (>= 4.4.0), SummarizedExperiment, methods
Imports: WGCNA, ica, moments, clusterProfiler, msigdbr, RColorBrewer,
        car, lme4, lmerTest, pheatmap, biomaRt, stats, grDevices,
        BiocParallel, ggplot2, patchwork, BiocGenerics, S4Vectors
Suggests: knitr, rmarkdown, testthat, biocViews, BiocCheck, BiocStyle,
        airway
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.2
VignetteBuilder: knitr
URL: https://github.com/jackgisby/ReducedExperiment
BugReports: https://github.com/jackgisby/ReducedExperiment/issues
biocViews: GeneExpression, Infrastructure, DataRepresentation,
        Software, DimensionReduction, Network
Config/pak/sysreqs: libcairo2-dev cmake libfontconfig1-dev
        libfreetype6-dev libglpk-dev make libicu-dev libpng-dev
        libxml2-dev libssl-dev zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-10-29 15:33:37 UTC
RemoteUrl: https://github.com/bioc/ReducedExperiment
RemoteRef: RELEASE_3_22
RemoteSha: 562222222db5356e2ab2eb29cdb93734012c413a
NeedsCompilation: no
Packaged: 2026-03-04 08:56:03 UTC; root
Author: Jack Gisby [aut, cre] (ORCID: <https://orcid.org/0000-0003-0511-8123>),
  Michael Barnes [aut] (ORCID: <https://orcid.org/0000-0001-9097-7381>)
Maintainer: Jack Gisby <jackgisby@gmail.com>
Built: R 4.5.2; ; 2026-03-04 08:58:28 UTC; windows
