Package: smartid
Title: Scoring and Marker Selection Method Based on Modified TF-IDF
Version: 1.9.0
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: 7.3.3
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), tibble, 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
Config/pak/sysreqs: cmake make libicu-dev libuv1-dev libssl-dev
        zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-04-28 13:02:43 UTC
RemoteUrl: https://github.com/bioc/smartid
RemoteRef: HEAD
RemoteSha: 931d9dfb23f0e58d026cfd08f1163699eafa3308
NeedsCompilation: no
Packaged: 2026-05-30 09:48:06 UTC; root
Author: Jinjin Chen [aut, cre] (ORCID: <https://orcid.org/0000-0001-7923-5723>)
Maintainer: Jinjin Chen <chen.j@wehi.edu.au>
Built: R 4.6.0; ; 2026-05-30 10:25:05 UTC; windows
