fmcsR

DOI: 10.18129/B9.bioc.fmcsR  

Mismatch Tolerant Maximum Common Substructure Searching

Bioconductor version: Release (3.16)

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 (version "4.2") 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")

 

HTML	R Script	fmcsR
PDF		Reference Manual
Text		README
Text		NEWS

Details

biocViews	BiomedicalInformatics, CellBasedAssays, Cheminformatics, Clustering, DataImport, Infrastructure, Metabolomics, MicrotitrePlateAssay, Pharmacogenetics, Pharmacogenomics, Proteomics, Software, Visualization
Version	1.40.0
In Bioconductor since	BioC 2.11 (R-2.15) (10.5 years)
License	Artistic-2.0
Depends	R (>= 2.10.0), ChemmineR, methods
Imports	RUnit, methods, ChemmineR, BiocGenerics, parallel
LinkingTo
Suggests	BiocStyle, knitr, knitcitations, knitrBootstrap, rmarkdown
SystemRequirements
Enhances
URL	https://github.com/girke-lab/fmcsR
Depends On Me
Imports Me	chemodiv
Suggests Me	ChemmineR
Links To Me
Build Report

Package Archives

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

Source Package	fmcsR_1.40.0.tar.gz
Windows Binary	fmcsR_1.40.0.zip (64-bit only)
macOS Binary (x86_64)	fmcsR_1.40.0.tgz
macOS Binary (arm64)	fmcsR_1.40.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/fmcsR
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/fmcsR
Bioc Package Browser	https://code.bioconductor.org/browse/fmcsR/
Package Short Url	https://bioconductor.org/packages/fmcsR/
Package Downloads Report	Download Stats