Package: octad
Title: Open Cancer TherApeutic Discovery (OCTAD)
Version: 1.6.0
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: 7.2.3
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
git_url: https://git.bioconductor.org/packages/octad
git_branch: RELEASE_3_19
git_last_commit: 4228d89
git_last_commit_date: 2024-04-30
Repository: Bioconductor 3.19
Date/Publication: 2024-04-30
NeedsCompilation: no
Packaged: 2024-05-01 05:55:46 UTC; biocbuild
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 4.4.0; ; 2024-05-01 13:54:22 UTC; unix
