octad
Open Cancer TherApeutic Discovery (OCTAD)
Bioconductor version: Release (3.20)
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>
citation("octad")):
Installation
To install this package, start R (version "4.4") 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")| octad | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Classification, GeneExpression, GeneSetEnrichment, Pharmacogenetics, Pharmacogenomics, Software |
| Version | 1.8.0 |
| In Bioconductor since | BioC 3.16 (R-4.2) (2 years) |
| License | Artistic-2.0 |
| 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 |
| System Requirements | |
| URL |
See More
| Suggests | knitr, rmarkdown |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | octad_1.8.0.tar.gz |
| Windows Binary (x86_64) | octad_1.8.0.zip |
| macOS Binary (x86_64) | octad_1.8.0.tgz |
| macOS Binary (arm64) | octad_1.7.0.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 |