DESCRIPTION

Package: ReducedExperiment
Type: Package
Title: Containers and tools for dimensionally-reduced -omics representations
Version: 0.99.6
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: 7.3.1
VignetteBuilder: knitr
URL: https://github.com/jackgisby/ReducedExperiment
BugReports: https://github.com/jackgisby/ReducedExperiment/issues
biocViews: GeneExpression, Infrastructure, DataRepresentation, Software,
    DimensionReduction, Network