mastR/DESCRIPTION at main · DavisLaboratory/mastR · GitHub

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Package: mastR
Title: Markers Automated Screening Tool in R
Version: 1.11.2
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