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.

19 exports 0.00 score 33 dependencies 195 downloads

Last updated 1 years agofrom:b031307ed0. Checks:OK: 1 WARNING: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKSep 01 2024
R-4.5-winWARNINGSep 01 2024
R-4.5-linuxWARNINGSep 01 2024
R-4.4-winWARNINGSep 01 2024
R-4.4-macWARNINGSep 01 2024
R-4.3-winWARNINGSep 01 2024
R-4.3-macWARNINGSep 01 2024

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

Dependencies:askpasscurlfingerprintherehttriteratorsitertoolsjsonliteKODAMAlatticeMatrixmimeminervaopensslpngR6rappdirsrcdkrcdklibsRcppRcppArmadilloRcppEigenRcppTOMLreticulaterJavarlangrprojrootRSpectraRtsnesysumapwithrXML

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 Sep 01 2024.

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