CONCERTDR/DESCRIPTION at main · DavidsonGroup/CONCERTDR · GitHub

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Package: CONCERTDR
Type: Package
Title: Drug Response Data Analysis Using CMap Database
Version: 0.99.1
Authors@R: c(
    person("Hengxin", "Pan",
        email = "pan.h@wehi.edu.au",
        role = c("aut", "cre"),
        comment = c(ORCID = "0009-0004-1274-1612")),
    person("Chin Wee", "Tan",
        email = "cwtan@wehi.edu.au",
        role = c("aut", "ths"),
        comment = c(ORCID = "0000-0001-9695-7218")),
    person("Gad", "Abraham",
        role = c("aut", "ths")),
    person("Nadia", "Davidson",
        email = "davidson.n@wehi.edu.au",
        role = c("aut", "ths"),
        comment = c(ORCID = "0000-0002-8461-7467"))
 )
Description: Provides a complete pipeline for drug repurposing analysis using
    the Connectivity Map (CMap) L1000 database. Functionality includes database
    subsetting, reference profile extraction from GCTX files, signature matching
    via Kolmogorov-Smirnov, GSEA-based, cosine similarity, and other methods,
    result annotation against CMap compound metadata, z-score matrix extraction,
    and publication-quality clustermap visualization via ComplexHeatmap.
    Connectivity scoring methods (KS, GSEA, XCos, XSum, Zhang) are implemented
    internally based on the algorithms described in Lamb et al. (2006),
    Subramanian et al. (2005), Cheng et al. (2014), and Zhang & Gant (2008),
    removing the need for external GitHub-only dependencies.
License: MIT + file LICENSE
Encoding: UTF-8
RoxygenNote: 7.3.3
URL: https://github.com/DavidsonGroup/CONCERT_DR
BugReports: https://github.com/DavidsonGroup/CONCERT_DR/issues
Depends:
    R (>= 4.5.0)
Imports:
    data.table,
    rhdf5,
    stats,
    utils
Suggests:
    knitr,
    rmarkdown,
    testthat,
    BiocStyle,
    ComplexHeatmap,
    circlize,
    ggplot2,
    RecordLinkage
VignetteBuilder: knitr
Config/testthat/edition: 3
biocViews:
    GeneExpression,
    Pharmacogenomics,
    Software,
    Transcriptomics,
    DataImport