fmcsR
This package is for version 3.19 of Bioconductor; for the stable, up-to-date release version, see fmcsR.
Mismatch Tolerant Maximum Common Substructure Searching
Bioconductor version: 3.19
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("fmcsR")):
Installation
To install this package, start R (version "4.4") 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 | ||
| README | Text | |
| NEWS | Text |
Details
| biocViews | BiomedicalInformatics, CellBasedAssays, Cheminformatics, Clustering, DataImport, Infrastructure, Metabolomics, MicrotitrePlateAssay, Pharmacogenetics, Pharmacogenomics, Proteomics, Software, Visualization |
| Version | 1.46.0 |
| In Bioconductor since | BioC 2.11 (R-2.15) (12 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 |
See More
| Suggests | BiocStyle, knitr, knitcitations, knitrBootstrap, rmarkdown |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | chemodiv |
| Suggests Me | ChemmineR, xnet |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | fmcsR_1.46.0.tar.gz |
| Windows Binary (x86_64) | fmcsR_1.46.0.zip (64-bit only) |
| macOS Binary (x86_64) | fmcsR_1.46.0.tgz |
| macOS Binary (arm64) | fmcsR_1.46.0.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 |