README.md

In Bin-Chen-Lab/octad: Open Cancer TherApeutic Discovery (OCTAD)

Web version:

http://octad.org/

How to install

OCTAD and OCTAD.db is now available on the bioconductor:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("octad")

Latest vestion is available on the github:

library(devtools)
install_github("Bin-Chen-Lab/octad.db")
install_github("Bin-Chen-Lab/octad")

Additional data

By default, octad package uses expression data for 978 genes from the LINCS dataset. However, it can influence the result and we advice using whole octad database. To obtatin whole results for DE, downloading of the additional OCTAD database octad.counts.and.tpm.h5 from the AWS link is required.

Examples

Example workflow can be found in the package vignette:

vignette('octad')

Contacts and citation

If you use our work, please cite the paper OCTAD: an open workplace for virtually screening therapeutics targeting precise cancer patient groups using gene expression features, Nature Protocols. Both OCTAD package and website was developed by Bin Chen laboratory. Examples and questions can be addressed to Eugene Chekalin, PhD, [e-mail] or Bin Chen, PhD, PI, [e-mail]

Bin-Chen-Lab/octad documentation built on Jan. 28, 2023, 11:20 p.m.