octad

DOI: 10.18129/B9.bioc.octad  

Open Cancer TherApeutic Discovery (OCTAD)

Bioconductor version: Release (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>

Installation

To install this package, start R (version "4.2") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("octad")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("octad")

 

HTML	R Script	octad
PDF		Reference Manual
Text		NEWS

Details

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
LinkingTo
Suggests	knitr, rmarkdown
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	octad_1.0.0.tar.gz
Windows Binary	octad_1.0.0.zip
macOS Binary (x86_64)	octad_1.0.0.tgz
macOS Binary (arm64)	octad_1.0.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/octad
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/octad
Bioc Package Browser	https://code.bioconductor.org/browse/octad/
Package Short Url	https://bioconductor.org/packages/octad/
Package Downloads Report	Download Stats