Package: MetChem 0.4

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>.

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]

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MetChem.pdf |MetChem.html✨
MetChem/json (API)

# Install 'MetChem' in R:
install.packages('MetChem', repos = c('https://tkcaccia.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Uses libs:
  • openjdk– OpenJDK Java runtime, using Hotspot JIT
Datasets:

On CRAN:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

openjdk

2.00 score 193 downloads 19 exports 34 dependencies

Last updated 2 years agofrom:b031307ed0. Checks:1 OK, 7 WARNING. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKJan 26 2025
R-4.5-winWARNINGJan 26 2025
R-4.5-macWARNINGJan 26 2025
R-4.5-linuxWARNINGJan 26 2025
R-4.4-winWARNINGJan 26 2025
R-4.4-macWARNINGJan 26 2025
R-4.3-winWARNINGJan 26 2025
R-4.3-macWARNINGJan 26 2025

Exports:allbrancheschemical.dissimilarityclusters.detectiondiseasesMetenzymesMetfeaturesKODAMA.chem.simnameMetpathwaysMetpropertiesMetreadMetselectionMetsubstituentsMettaxonomyMettree.cuttingWMCSAwrite.clswrite.gctwrite.gmt

Dependencies:askpasscurlfingerprintherehttriteratorsitertoolsjsonliteKODAMAlatticeMatrixmimeminervaopensslpngR6rappdirsrcdkrcdklibsRcppRcppArmadilloRcppEigenRcppTOMLreticulaterJavarlangRnanoflannrprojrootRSpectraRtsnesysumapwithrXML

A new pipeline to explore structural similarity across metabolite modules

| Ebtesam Abdel-Shafy, Tadele Melak, David A. MacIntyre, | Giorgia Zadra, Luiz F. Zerbini, Silvano Piazza, and Stefano Cacciatore

Rendered fromMetChem.Rmdusingknitr::knitron Jan 26 2025.

Last update: 2023-07-06
Started: 2022-12-20