Package: CONCERTDR
Type: Package
Title: Drug Response Data Analysis Using CMap Database
Version: 0.99.2
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/CONCERTDR
BugReports: https://github.com/DavidsonGroup/CONCERTDR/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
Config/pak/sysreqs: libssl-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-08-13 03:32:27 UTC
RemoteUrl: https://github.com/bioc/CONCERTDR
RemoteRef: HEAD
RemoteSha: d27d37cc7cfff088069a80ddad5482a20923cc08
NeedsCompilation: no
Packaged: 2026-10-11 10:31:18 UTC; root
Author: Hengxin Pan [aut, cre] (ORCID: <https://orcid.org/0009-0004-1274-1612>),
  Chin Wee Tan [aut, ths] (ORCID:
    <https://orcid.org/0000-0001-9695-7218>),
  Gad Abraham [aut, ths],
  Nadia Davidson [aut, ths] (ORCID:
    <https://orcid.org/0000-0002-8461-7467>)
Maintainer: Hengxin Pan <pan.h@wehi.edu.au>