Package: octad
Title: Open Cancer TherApeutic Discovery (OCTAD)
Version: 1.12.0
Authors@R: 
    c(person(given = "E.",
           family = "Chekalin",
           role = c("aut", "cre"),
           email = "eygen.chekalin@gmail.com"),
           person(given = "S.",
           family = "Paithankar",role =c("aut")),
           person(given = "B.",
           family = "Zeng",role =c("aut")),
           person(given = "B.",
           family = "Glicksberg",role ="ctb"),
           person(given = "P.",
           family = "Newbury",role ="ctb"),
           person(given = "J.",
           family = "Xing",role ="ctb"),
           person(given = "K.",
           family = "Liu",role ="ctb"),
           person(given = "A.",
           family = "Wen",role ="ctb"),
            person(given = "D.",
           family = "Joseph",role ="ctb"),
           person(given = "B.",
           family = "Chen",
           role ="aut",
           email = "chenbi12@msu.edu")
           )
Description: OCTAD provides a platform for virtually screening
        compounds targeting precise cancer patient groups. The
        essential idea is to identify drugs that reverse the gene
        expression signature of disease by tamping down over-expressed
        genes and stimulating weakly expressed ones. The package offers
        deep-learning based reference tissue selection, disease gene
        expression signature creation, pathway enrichment analysis,
        drug reversal potency scoring, cancer cell line selection, drug
        enrichment analysis and in silico hit validation. It currently
        covers ~20,000 patient tissue samples covering 50 cancer types,
        and expression profiles for ~12,000 distinct compounds.
License: Artistic-2.0
Encoding: UTF-8
LazyData: FALSE
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.2
Depends: R (>= 4.2.0), magrittr, dplyr, ggplot2, edgeR, RUVSeq, DESeq2,
        limma, rhdf5, foreach, Rfast, octad.db, stats, httr, qpdf,
        ExperimentHub, AnnotationHub, Biobase, S4Vectors
Imports: EDASeq, GSVA, data.table, htmlwidgets, plotly, reshape2,
        grDevices, utils
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
biocViews: Classification, GeneExpression, Pharmacogenetics,
        Pharmacogenomics, Software, GeneSetEnrichment
Config/pak/sysreqs: make libmagick++-dev gsfonts libbz2-dev libicu-dev
        libjpeg-dev liblzma-dev libpng-dev libxml2-dev libssl-dev
        xz-utils zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-10-29 15:19:54 UTC
RemoteUrl: https://github.com/bioc/octad
RemoteRef: RELEASE_3_22
RemoteSha: e8beea048baf292eba9ff55d0e8e829da7b7551e
NeedsCompilation: no
Packaged: 2025-11-20 07:33:46 UTC; root
Author: E. Chekalin [aut, cre],
  S. Paithankar [aut],
  B. Zeng [aut],
  B. Glicksberg [ctb],
  P. Newbury [ctb],
  J. Xing [ctb],
  K. Liu [ctb],
  A. Wen [ctb],
  D. Joseph [ctb],
  B. Chen [aut]
Maintainer: E. Chekalin <eygen.chekalin@gmail.com>
Built: R 4.5.2; ; 2025-11-20 07:37:00 UTC; windows
