fmcsR

This package is for version 3.7 of Bioconductor; for the stable, up-to-date release version, see fmcsR.

Mismatch Tolerant Maximum Common Substructure Searching

Bioconductor version: 3.7

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>

Citation (from within R, enter citation("fmcsR")):

Installation

To install this package, start R (version "3.5") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("fmcsR")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("fmcsR")

fmcsR	HTML	R Script
Reference Manual	PDF
README	Text
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	BiomedicalInformatics, CellBasedAssays, Cheminformatics, Clustering, DataImport, Infrastructure, MicrotitrePlateAssay, Pharmacogenetics, Pharmacogenomics, Proteomics, Software, Visualization
Version	1.22.0
In Bioconductor since	BioC 2.11 (R-2.15) (11.5 years)
License	Artistic-2.0
Depends	R (>= 2.10.0), ChemmineR, methods
Imports	RUnit, methods, ChemmineR, BiocGenerics, parallel
System Requirements
URL	https://github.com/girke-lab/fmcsR

Suggests	BiocStyle, knitr, knitcitations, knitrBootstrap
Linking To
Enhances
Depends On Me
Imports Me	Rcpi
Suggests Me	ChemmineR
Links To Me
Build Report	Build Report

Package Archives

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

Source Package	fmcsR_1.22.0.tar.gz
Windows Binary	fmcsR_1.22.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan)	fmcsR_1.22.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/fmcsR
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/fmcsR
Package Short Url	https://bioconductor.org/packages/fmcsR/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.7	Source Archive