customCMPdb: Integrating Community and Custom Compound Collections

Introduction

This package serves as a query interface for important community collections of small molecules, while also allowing users to include custom compound collections. At the time of writing, the following community databases are included:

• DrugAge
• DrugBank
• CMAP02
• LINCS

Installation and Loading

customCMPdb is an R/Bioconductor package and can be installed using BiocManager::install().

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

To obtain the most recent updates immediately, one can install it directly from GitHub as follows.

devtools::install_github("yduan004/customCMPdb", build_vignettes=TRUE)

After the package is installed, it can be loaded into an R session as follows.

library(customCMPdb)

For detailed description of the package, please refer to the vignette by running

browseVignettes("customCMPdb")

Vignette

The vignette of this package is also available at here