DESCRIPTION

Package: lute
Version: 1.1.1
Title: Framework for cell size scale factor normalized bulk transcriptomics deconvolution experiments
Authors@R: c(
    person(c("Sean", "K"), "Maden", role = c("cre", "aut"), 
            email = "maden.sean@gmail.com", comment = c(ORCID = "0000-0002-2212-4894")),
    person("Stephanie", "Hicks", role = "aut", 
            email = "shicks19@gmail.com", comment = c(ORCID = "0000-0002-7858-0231")))
Description: Provides a framework for adjustment on cell type size when performing bulk transcripomics deconvolution. The main framework function provides a means of reference normalization using cell size scale factors. It allows for marker selection and deconvolution using non-negative least squares (NNLS) by default. The framework is extensible for other marker selection and deconvolution algorithms, and users may reuse the generics, methods, and classes for these when developing new algorithms.
License: Artistic-2.0
Encoding: UTF-8
URL: https://github.com/metamaden/lute
BugReports: https://github.com/metamaden/lute/issues
LazyData: FALSE
Depends:
    R (>= 4.3.0),
    stats,
    methods,
    utils,
    SummarizedExperiment,
    SingleCellExperiment,
    BiocGenerics
Imports:
    S4Vectors,
    Biobase,
    scran,
    dplyr,
    ggplot2
Suggests:
    nnls, 
    knitr,
    testthat,
    rmarkdown,
    BiocStyle,
    GenomicRanges,
    limma,
    ExperimentHub,
    AnnotationHub,
    DelayedMatrixStats,
    BisqueRNA,
    DelayedArray
VignetteBuilder:
    knitr
biocViews: RNASeq, Sequencing, SingleCell, Coverage, Transcriptomics, Normalization
RoxygenNote: 7.3.1
Collate: 
    'lute_generics.R'
    'deconvolutionParam-class.R'
    'referencebasedParam-class.R'
    'independentbulkParam-class.R'
    'bisqueParam-class.R'
    'typemarkersParam-class.R'
    'findmarkersParam-class.R'
    'globals.R'
    'lute_cellScaleFactors.R'
    'lute_classes.R'
    'lute_conversions.R'
    'lute_framework.R'
    'lute_metadata.R'
    'lute_randomized-data.R'
    'lute_rmse.R'
    'lute_rnf.R'
    'lute_utilities.R'
    'nnlsParam-class.R'