Package: octad
Title: Open Cancer TherApeutic Discovery (OCTAD)
Version: 1.15.1
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: 7.3.3
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/Bioconductor/UnsupportedPlatforms: windows
Config/pak/sysreqs: cmake make libmagick++-dev gsfonts libbz2-dev
        libicu-dev libjpeg-dev liblzma-dev libpng-dev libuv1-dev
        libxml2-dev libssl-dev xz-utils zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-05-29 18:37:21 UTC
RemoteUrl: https://github.com/bioc/octad
RemoteRef: HEAD
RemoteSha: b39886ce482f24b666cd7eef0cfc3fd1ca1ee8b7
NeedsCompilation: no
Packaged: 2026-07-05 14:02:51 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>