Package: mastR
Title: Markers Automated Screening Tool in R
Version: 1.12.0
Authors@R: 
    c(
     person("Jinjin", "Chen", email = "chen.j@wehi.edu.au", role = c("aut", "cre"), comment = c(ORCID = "0000-0001-7923-5723")),
     person("Ahmed", "Mohamed", email = "mohamed.a@wehi.edu.au", role = c("aut", "ctb"), comment = c(ORCID = "0000-0001-6507-5300")),
     person("Chin Wee", "Tan", email = "cwtan@wehi.edu.au", role = c("ctb"), comment = c(ORCID = "0000-0001-9695-7218"))
    )
Description: mastR is an R package designed for automated screening of
        signatures of interest for specific research questions. The
        package is developed for generating refined lists of signature
        genes from multiple group comparisons based on the results from
        edgeR and limma differential expression (DE) analysis workflow.
        It also takes into account the background noise of
        tissue-specificity, which is often ignored by other marker
        generation tools. This package is particularly useful for the
        identification of group markers in various biological and
        medical applications, including cancer research and
        developmental biology.
biocViews: Software, GeneExpression, Transcriptomics,
        DifferentialExpression, Visualization
License: MIT + file LICENSE
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.2
Depends: R (>= 4.3.0)
Suggests: BiocManager, BiocStyle, clusterProfiler, ComplexHeatmap,
        depmap, enrichplot, ggrepel, ggvenn, Glimma, gridExtra,
        jsonlite, knitr, rmarkdown, RobustRankAggreg, rvest, scuttle,
        singscore, splatter, testthat (>= 3.0.0), UpSetR
Config/testthat/edition: 3
Imports: AnnotationDbi, Biobase, dplyr, edgeR, ggplot2, ggpubr,
        graphics, grDevices, GSEABase, limma, Matrix, methods, msigdb,
        org.Hs.eg.db, patchwork, SeuratObject (> 5.0.0),
        SingleCellExperiment, stats, SummarizedExperiment, tidyr, utils
Collate: 'plot.R' 'DE_functions.R' 'AllGenerics.R'
        'filter_subset_sig-methods.R' 'get_de_table-methods.R'
        'get_degs-methods.R' 'get_gsc_sig-methods.R' 'get_lm_sig.R'
        'get_panglao_sig.R' 'gls2gsc-methods.R' 'gsc_plot.R'
        'list_panglao_organs.R' 'list_panglao_types.R'
        'mastR-package.R' 'merge_markers.R' 'pca_matrix_plot-methods.R'
        'pseudo_samples-methods.R' 'remove_bg_exp-methods.R'
        'sig_boxplot-methods.R' 'sig_gseaplot-methods.R'
        'sig_heatmap-methods.R' 'sig_rankdensity_plot-methods.R'
        'sig_scatter_plot-methods.R' 'subset_sig_by_step.R'
URL: https://davislaboratory.github.io/mastR
BugReports: https://github.com/DavisLaboratory/mastR/issues
VignetteBuilder: knitr
Language: en-US
Config/pak/sysreqs: cmake make libicu-dev libpng-dev libxml2-dev
        libssl-dev zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2026-04-28 13:00:37 UTC
RemoteUrl: https://github.com/bioc/mastR
RemoteRef: RELEASE_3_23
RemoteSha: 9b05459fa70f898a80415119b7a20d2acc1f1803
NeedsCompilation: no
Packaged: 2026-04-29 23:16:41 UTC; root
Author: Jinjin Chen [aut, cre] (ORCID: <https://orcid.org/0000-0001-7923-5723>),
  Ahmed Mohamed [aut, ctb] (ORCID:
    <https://orcid.org/0000-0001-6507-5300>),
  Chin Wee Tan [ctb] (ORCID: <https://orcid.org/0000-0001-9695-7218>)
Maintainer: Jinjin Chen <chen.j@wehi.edu.au>
Built: R 4.6.0; ; 2026-04-29 23:21:39 UTC; windows
