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")
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.
Example workflow can be found in the package vignette:
vignette('octad')
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, [email protected] or Bin Chen, PhD, PI, [email protected]