MetChem: Chemical Structural Similarity Analysis

A new pipeline to explore chemical structural similarity across metabolite. It allows to classify metabolites in structurally-related modules and identify common shared functional groups. 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: 0.4
Depends: R (≥ 3.5.0), stats, KODAMA (≥ 2.3), httr, XML, fingerprint, rcdk (≥ 3.4.3)
Suggests: knitr, rmarkdown, readxl, impute, pheatmap, RColorBrewer
Published: 2023-07-06
DOI: NA
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
CRAN checks: MetChem results

Documentation:

Reference manual: MetChem.pdf
Vignettes: A simple pipeline to explore structural similarities between metabolites

Downloads:

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

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