Package: ReducedExperiment
Type: Package
Title: Containers and tools for dimensionally-reduced -omics
        representations
Version: 1.1.2
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
git_url: https://git.bioconductor.org/packages/ReducedExperiment
git_branch: devel
git_last_commit: 31e725b
git_last_commit_date: 2025-05-22
Repository: Bioconductor 3.22
Date/Publication: 2025-06-04
NeedsCompilation: no
Packaged: 2025-06-05 01:36:05 UTC; biocbuild
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 4.5.0; ; 2025-06-05 13:48:29 UTC; windows
