IDEAS home Printed from https://ideas.repec.org/a/jss/jstsof/v018i05.html
   My bibliography  Save this article

Chemical Informatics Functionality in R

Author

Listed:
  • Guha, Rajarshi

Abstract

The flexibility and scope of the R programming environment has made it a popular choice for statistical modeling and scientific prototyping in a number of fields. In the field of chemistry, R provides several tools for a variety of problems related to statistical modeling of chemical information. However, one aspect common to these tools is that they do not have direct access to the information that is available from chemical structures, such as contained in molecular descriptors. We describe the rcdk package that provides the R user with access to the CDK, a Java framework for cheminformatics. As a result, it is possible to read in a variety of molecular formats, calculate molecular descriptors and evaluate fingerprints. In addition, we describe the rpubchem that will allow access to the data in PubChem, a public repository of molecular structures and associated assay data for approximately 8 million compounds. Currently, the package allows access to structural information as well as some simple molecular properties from PubChem. In addition the package allows access to bio-assay data from the PubChem FTP servers.

Suggested Citation

  • Guha, Rajarshi, 2007. "Chemical Informatics Functionality in R," Journal of Statistical Software, Foundation for Open Access Statistics, vol. 18(i05).
    • Handle: RePEc:jss:jstsof:v:018:i05
    DOI: http://hdl.handle.net/10.18637/jss.v018.i05
    as

    Download full text from publisher

    File URL: https://www.jstatsoft.org/index.php/jss/article/view/v018i05/v18i05.pdf
    Download Restriction: no
    File URL: https://www.jstatsoft.org/index.php/jss/article/downloadSuppFile/v018i05/Data.zip
    Download Restriction: no
    File URL: https://www.jstatsoft.org/index.php/jss/article/downloadSuppFile/v018i05/rcdk_2.6.1.tar.gz
    Download Restriction: no
    File URL: https://www.jstatsoft.org/index.php/jss/article/downloadSuppFile/v018i05/rpubchem_1.4.tar.gz
    Download Restriction: no
    File URL: https://www.jstatsoft.org/index.php/jss/article/downloadSuppFile/v018i05/v18i05.R.zip
    Download Restriction: no
    File URL: https://libkey.io/http://hdl.handle.net/10.18637/jss.v018.i05?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    Citations

    Citations are extracted by the CitEc Project, subscribe to its RSS feed for this item.
    as


    Cited by:

    1. Mullen, Katharine M. & van Stokkum, Ivo H. M., 2007. "An Introduction to the "Special Volume Spectroscopy and Chemometrics in R"," Journal of Statistical Software, Foundation for Open Access Statistics, vol. 18(i01).
    2. Alina Bărbulescu & Lucica Barbeș & Cristian Ștefan Dumitriu, 2022. "Computer-Aided Methods for Molecular Classification," Mathematics, MDPI, vol. 10(9), pages 1-19, May.
    3. repec:jss:jstsof:18:i01 is not listed on IDEAS
    4. Jenna E. Leeuwen & Wail Ba-Alawi & Emily Branchard & Jennifer Cruickshank & Wiebke Schormann & Joseph Longo & Jennifer Silvester & Peter L. Gross & David W. Andrews & David W. Cescon & Benjamin Haibe-, 2022. "Computational pharmacogenomic screen identifies drugs that potentiate the anti-breast cancer activity of statins," Nature Communications, Nature, vol. 13(1), pages 1-17, December.
    5. Anna Cichonska & Balaguru Ravikumar & Elina Parri & Sanna Timonen & Tapio Pahikkala & Antti Airola & Krister Wennerberg & Juho Rousu & Tero Aittokallio, 2017. "Computational-experimental approach to drug-target interaction mapping: A case study on kinase inhibitors," PLOS Computational Biology, Public Library of Science, vol. 13(8), pages 1-28, August.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:jss:jstsof:v:018:i05. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    We have no bibliographic references for this item. You can help adding them by using this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Christopher F. Baum (email available below). General contact details of provider: http://www.jstatsoft.org/ .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.