DOI: 10.18129/B9.bioc.octad  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see octad.

Open Cancer TherApeutic Discovery (OCTAD)

Bioconductor version: 3.16

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.

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 at gmail.com>

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biocViews Classification, GeneExpression, GeneSetEnrichment, Pharmacogenetics, Pharmacogenomics, Software
Version 1.0.0
In Bioconductor since BioC 3.16 (R-4.2) (< 6 months)
License Artistic-2.0
Depends R (>= 4.2.0), magrittr, dplyr, ggplot2, edgeR, RUVSeq, DESeq2, limma, rhdf5, foreach, Rfast, octad.db, stats, httr, ExperimentHub, AnnotationHub, Biobase, S4Vectors
Imports EDASeq, GSVA, data.table, htmlwidgets, plotly, reshape2, grDevices, utils
Suggests knitr, rmarkdown
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Source Package octad_1.0.0.tar.gz
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