README.md

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Overview

Rcpi offers a molecular informatics toolkit with a comprehensive integration of bioinformatics and cheminformatics tools for drug discovery. For more information, please see our paper <DOI:10.1093/bioinformatics/btu624> (PDF).

Paper Citation

Formatted citation:

Dong-Sheng Cao, Nan Xiao, Qing-Song Xu, and Alex F. Chen. (2015). Rcpi: R/Bioconductor package to generate various descriptors of proteins, compounds and their interactions. Bioinformatics 31 (2), 279-281.

BibTeX entry:

@article{Rcpi2015,
  author = {Cao, Dong-Sheng and Xiao, Nan and Xu, Qing-Song and Alex F. Chen.},
  title = {{Rcpi: R/Bioconductor package to generate various descriptors of proteins, compounds and their interactions}},
  journal = {Bioinformatics},
  year = {2015},
  volume = {31},
  number = {2},
  pages = {279--281},
  doi = {10.1093/bioinformatics/btu624},
  issn = {1367-4803},
  url = {http://bioinformatics.oxfordjournals.org/content/31/2/279}
}

Installation

To install the Rcpi package:

install.packages("BiocManager")
BiocManager::install("Rcpi")

To make the package fully functional (especially the Open Babel related functions), we recommend installing the Enhances packages by:

BiocManager::install("Rcpi", dependencies = c("Imports", "Enhances"))

Several dependencies of the Rcpi package may require some system-level libraries, check the corresponding manuals of these packages for detailed installation guides.

Browse the package vignettes: [1], [2] for a quick-start.

Features

Rcpi implemented and integrated the state-of-the-art protein sequence descriptors and molecular descriptors/fingerprints with R. For protein sequences, the Rcpi package could

For small molecules, the Rcpi package could

By combining various types of descriptors for drugs and proteins in different methods, interaction descriptors representing protein-protein or compound-protein interactions could be conveniently generated with Rcpi, including:

Several useful auxiliary utilities are also shipped with Rcpi:

The computed protein sequence descriptors, molecular descriptors/fingerprints, interaction descriptors and pairwise similarities are widely used in various research fields relevant to drug disvery, primarily bioinformatics, cheminformatics, proteochemometrics, and chemogenomics.

Contribute

To contribute to this project, please take a look at the Contributing Guidelines first. Please note that this project is released with a Contributor Code of Conduct. By participating in this project you agree to abide by its terms.



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Rcpi documentation built on July 18, 2018, 10 a.m.