Package: TREG
Title: Tools for finding Total RNA Expression Genes in single nucleus
        RNA-seq data
Version: 1.13.0
Date: 2023-06-16
Authors@R: 
    c(person(given = "Louise",
           family = "Huuki-Myers",
           role = c("aut", "cre"),
           email = "lahuuki@gmail.com",
           comment = c(ORCID = "0000-0001-5148-3602")),
    person("Leonardo", "Collado-Torres", role = c("ctb"), 
    email = "lcolladotor@gmail.com", comment = c(ORCID = "0000-0003-2140-308X"))
    )
Description: RNA abundance and cell size parameters could improve RNA-seq
    deconvolution algorithms to more accurately estimate cell type proportions
    given the different cell type transcription activity levels. A Total RNA
    Expression Gene (TREG) can facilitate estimating total RNA content using
    single molecule fluorescent in situ hybridization (smFISH). We developed a
    data-driven approach using a measure of expression invariance to find
    candidate TREGs in postmortem human brain single nucleus RNA-seq. This R
    package implements the method for identifying candidate TREGs from
    snRNA-seq data.
License: Artistic-2.0
URL: https://github.com/LieberInstitute/TREG,
        http://research.libd.org/TREG/
BugReports: https://support.bioconductor.org/t/TREG
biocViews: Software, SingleCell, RNASeq, GeneExpression,
        Transcriptomics, Transcription, Sequencing
Encoding: UTF-8
LazyData: true
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.2.3
Depends: R (>= 4.2), SummarizedExperiment
Suggests: BiocFileCache, BiocStyle, dplyr, ggplot2, knitr, pheatmap,
        sessioninfo, RefManageR, rmarkdown, testthat (>= 3.0.0),
        tibble, tidyr, SingleCellExperiment
Config/testthat/edition: 3
Imports: Matrix, purrr, rafalib
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/TREG
git_branch: devel
git_last_commit: a725a2d
git_last_commit_date: 2025-04-15
Repository: Bioconductor 3.22
Date/Publication: 2025-06-04
NeedsCompilation: no
Packaged: 2025-06-05 02:41:33 UTC; biocbuild
Author: Louise Huuki-Myers [aut, cre] (ORCID:
    <https://orcid.org/0000-0001-5148-3602>),
  Leonardo Collado-Torres [ctb] (ORCID:
    <https://orcid.org/0000-0003-2140-308X>)
Maintainer: Louise Huuki-Myers <lahuuki@gmail.com>
Built: R 4.5.0; ; 2025-06-05 14:15:24 UTC; windows
