Package: smartid
Title: Scoring and Marker Selection Method Based on Modified TF-IDF
Version: 1.7.0
Authors@R: 
    person("Jinjin", "Chen", email = "chen.j@wehi.edu.au", role = c("aut", "cre"),
           comment = c(ORCID = "0000-0001-7923-5723"))
Description: This package enables automated selection of group specific
    signature, especially for rare population. The package is developed for
    generating specifc lists of signature genes based on Term Frequency-Inverse
    Document Frequency (TF-IDF) modified methods. It can also be used as a new
    gene-set scoring method or data transformation method. Multiple visualization
    functions are implemented in this package.
biocViews: Software, GeneExpression, Transcriptomics
License: MIT + file LICENSE
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.2
Collate: 
    'AllClasses.R'
    'tf_idf_iae_wrappers.R'
    'score.R'
    'AllGenerics.R'
    'gs_score-methods.R'
    'plot.R'
    'scale_mgm.R'
    'smartid-package.R'
    'score-methods.R'
    'select_markers.R'
    'top_markers.R'
    'top_markers-methods.R'
Depends: 
    R (>= 4.4)
Imports: 
    dplyr,
    ggplot2,
    graphics,
    Matrix,
    mclust,
    methods,
    mixtools,
    sparseMatrixStats,
    stats,
    SummarizedExperiment,
    tidyr,
    utils
Suggests: 
    BiocStyle,
    dbscan,
    ggpubr,
    knitr,
    rmarkdown,
    scater,
    splatter,
    testthat (>= 3.0.0),
    tidytext,
    UpSetR
URL: https://davislaboratory.github.io/smartid
BugReports: https://github.com/DavisLaboratory/smartid/issues
VignetteBuilder: knitr
Language: en-US
Config/testthat/edition: 3
LazyData: false
git_url: https://git.bioconductor.org/packages/smartid
git_branch: devel
git_last_commit: c55bd41
git_last_commit_date: 2025-10-29
Repository: Bioconductor 3.23
