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 , Cacciatore S, Luchinat C, Tenori L. (2014) Proc Natl Acad Sci USA , and Abdel-Shafy EA, Melak T, MacIntyre DA, Zadra G, Zerbini LF, Piazza S, Cacciatore S. (2023) Bioinformatics Advances .


MetChem

This is a pipeline to explore structural similarity across metabolite network

Reference manual

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install.packages("MetChem")

0.5 by Stefano Cacciatore, a year ago


Browse source code at https://github.com/cran/MetChem


Authors: 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]


Documentation:   PDF Manual  


GPL (>= 2) license


Depends on stats, KODAMA, httr, XML, fingerprint, rcdk

Suggests knitr, rmarkdown, readxl, impute, pheatmap, RColorBrewer, clinical


See at CRAN