Package: lute
Version: 1.4.0
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
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'
git_url: https://git.bioconductor.org/packages/lute
git_branch: RELEASE_3_21
git_last_commit: 5add22a
git_last_commit_date: 2025-04-15
Repository: Bioconductor 3.21
Date/Publication: 2025-04-15
NeedsCompilation: no
Packaged: 2025-04-16 01:39:48 UTC; biocbuild
Author: Sean K Maden [cre, aut] (ORCID:
    <https://orcid.org/0000-0002-2212-4894>),
  Stephanie Hicks [aut] (ORCID: <https://orcid.org/0000-0002-7858-0231>)
Maintainer: Sean K Maden <maden.sean@gmail.com>
Built: R 4.5.0; ; 2025-04-16 14:47:24 UTC; windows
