Rajarshi Guha

Rajarshi Guha

7 packages on CRAN

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Functions to manipulate binary fingerprints of arbitrary length. A fingerprint is represented by an object of S4 class 'fingerprint' which is internally represented a vector of integers, such that each element represents the position in the fingerprint that is set to 1. The bitwise logical functions in R are overridden so that they can be used directly with 'fingerprint' objects. A number of distance metrics are also available (many contributed by Michael Fadock). Fingerprints can be converted to Euclidean vectors (i.e., points on the unit hypersphere) and can also be folded using OR. Arbitrary fingerprint formats can be handled via line handlers. Currently handlers are provided for CDK, MOE and BCI fingerprint data.

rpubchem

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Access PubChem data (compounds, substance, assays) using R. Structural information is provided in the form of SMILES strings. It currently only provides access to a subset of the precalculated data stored by PubChem. Bio-assay data can be accessed to obtain descriptions as well as the actual data. It is also possible to search for assay ID's by keyword.

spe

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Implements stochastic proximity embedding as described by Agrafiotis et al. in PNAS, 2002, 99, pg 15869 and J. Comput. Chem., 2003,24, pg 1215

foreign

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Reading and writing data stored by some versions of 'Epi Info', 'Minitab', 'S', 'SAS', 'SPSS', 'Stata', 'Systat', 'Weka', and for reading and writing some 'dBase' files.

pmml

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The Predictive Model Markup Language (PMML) is an XML-based language which provides a way for applications to define machine learning, statistical and data mining models and to share models between PMML compliant applications. More information about the PMML industry standard and the Data Mining Group can be found at <http://www.dmg.org>. The generated PMML can be imported into any PMML consuming application, such as Zementis Predictive Analytics products, which integrate with web services, relational database systems and deploy natively on Hadoop in conjunction with Hive, Spark or Storm, as well as allow predictive analytics to be executed for IBM z Systems mainframe applications and real-time, streaming analytics platforms. The package isofor (used for anomaly detection) can be installed with devtools::install_github("Zelazny7/isofor").

rcdk

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Allows the user to access functionality in the 'CDK', a Java framework for chemoinformatics. This allows the user to load molecules, evaluate fingerprints, calculate molecular descriptors and so on. In addition, the 'CDK' API allows the user to view structures in 2D.

rcdklibs

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An R interface to the Chemistry Development Kit, a Java library for chemoinformatics. Given the size of the library itself, this package is not expected to change very frequently. To make use of the CDK within R, it is suggested that you use the 'rcdk' package. Note that it is possible to directly interact with the CDK using 'rJava'. However 'rcdk' exposes functionality in a more idiomatic way. The CDK library itself is released as LGPL and the sources can be obtained from <https://github.com/cdk/cdk>.