MetChem: Chemical Structural Similarity Analysis

A new pipeline to explore chemical structural similarity across metabolites. It allows the metabolite classification in structurally-related modules and identifies common shared functional groups. The KODAMA algorithm is used to highlight structural similarity between metabolites. See Cacciatore S, Tenori L, Luchinat C, Bennett PR, MacIntyre DA. (2017) Bioinformatics <doi:10.1093/bioinformatics/btw705>, Cacciatore S, Luchinat C, Tenori L. (2014) Proc Natl Acad Sci USA <doi:10.1073/pnas.1220873111>, and Abdel-Shafy EA, Melak T, MacIntyre DA, Zadra G, Zerbini LF, Piazza S, Cacciatore S. (2023) Bioinformatics Advances <doi:10.1093/bioadv/vbad053>.

Version: 0.5
Depends: R (≥ 3.5.0), stats, KODAMA (≥ 3.0), httr, XML, fingerprint, rcdk (≥ 3.4.3)
Suggests: knitr, rmarkdown, readxl, impute, pheatmap, RColorBrewer, clinical
Published: 2025-06-04
DOI: 10.32614/CRAN.package.MetChem
Author: Ebtesam Abdel-Shafy [aut], Tadele Melak [aut], David A. MacIntyre [aut], Giorgia Zadra [aut], Luiz F. Zerbini [aut], Silvano Piazza [aut], Stefano Cacciatore [aut, cre]
Maintainer: Stefano Cacciatore <tkcaccia at gmail.com>
License: GPL-2 | GPL-3 [expanded from: GPL (≥ 2)]
NeedsCompilation: no
Materials: README
CRAN checks: MetChem results

Documentation:

Reference manual: MetChem.pdf
Vignettes: A simple pipeline to explore structural similarities between metabolites (source, R code)

Downloads:

Package source: MetChem_0.5.tar.gz
Windows binaries: r-devel: MetChem_0.5.zip, r-release: MetChem_0.4.zip, r-oldrel: MetChem_0.4.zip
macOS binaries: r-release (arm64): MetChem_0.5.tgz, r-oldrel (arm64): MetChem_0.5.tgz, r-release (x86_64): MetChem_0.5.tgz, r-oldrel (x86_64): MetChem_0.5.tgz
Old sources: MetChem archive

Linking:

Please use the canonical form https://CRAN.R-project.org/package=MetChem to link to this page.