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>

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

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

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: