Package: MetChem 0.4

Stefano Cacciatore

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]

MetChem_0.4.tar.gz
MetChem_0.4.tar.gz(r-4.5-noble)MetChem_0.4.tar.gz(r-4.4-noble)
MetChem_0.4.tgz(r-4.4-emscripten)MetChem_0.4.tgz(r-4.3-emscripten)
MetChem.pdf |MetChem.html
MetChem/json (API)

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

Peer review:

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

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

openjdk

2.00 score 172 downloads 19 exports 33 dependencies

Last updated 1 years agofrom:b031307ed0. Checks:OK: 1 WARNING: 1. Indexed: no.

TargetResultDate
Doc / VignettesOKDec 03 2024
R-4.5-linuxWARNINGDec 03 2024

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

Dependencies:askpasscurlfingerprintherehttriteratorsitertoolsjsonliteKODAMAlatticeMatrixmimeminervaopensslpngR6rappdirsrcdkrcdklibsRcppRcppArmadilloRcppEigenRcppTOMLreticulaterJavarlangrprojrootRSpectraRtsnesysumapwithrXML

A new pipeline to explore structural similarity across metabolite modules

Rendered fromMetChem.Rmdusingknitr::knitron Dec 03 2024.

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