fmcsR

DOI: 10.18129/B9.bioc.fmcsR    

Mismatch Tolerant Maximum Common Substructure Searching

Bioconductor version: Release (3.6)

The fmcsR package introduces an efficient maximum common substructure (MCS) algorithms combined with a novel matching strategy that allows for atom and/or bond mismatches in the substructures shared among two small molecules. The resulting flexible MCSs (FMCSs) are often larger than strict MCSs, resulting in the identification of more common features in their source structures, as well as a higher sensitivity in finding compounds with weak structural similarities. The fmcsR package provides several utilities to use the FMCS algorithm for pairwise compound comparisons, structure similarity searching and clustering.

Author: Yan Wang, Tyler Backman, Kevin Horan, Thomas Girke

Maintainer: Thomas Girke <thomas.girke at ucr.edu>

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("fmcsR")

Documentation

HTML	R Script	fmcsR
PDF		Reference Manual
Text		README
Text		NEWS

Details

biocViews	BiomedicalInformatics, CellBasedAssays, Cheminformatics, Clustering, DataImport, Infrastructure, MicrotitrePlateAssay, Pharmacogenetics, Pharmacogenomics, Proteomics, Software, Visualization
Version	1.20.0
In Bioconductor since	BioC 2.11 (R-2.15) (5.5 years)
License	Artistic-2.0
Depends	R (>= 2.10.0), ChemmineR, methods
Imports	RUnit, methods, ChemmineR, BiocGenerics, parallel
LinkingTo
Suggests	BiocStyle, knitr, knitcitations, knitrBootstrap
SystemRequirements
Enhances
URL	https://github.com/girke-lab/fmcsR
Depends On Me
Imports Me	BioMedR, Rcpi
Suggests Me	ChemmineR
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	fmcsR_1.20.0.tar.gz
Windows Binary	fmcsR_1.20.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan)	fmcsR_1.20.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/fmcsR
Package Short Url	http://bioconductor.org/packages/fmcsR/
Package Downloads Report	Download Stats