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:
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')) |
- ChemRICH - ChemRICH Dataset
- HFD - HFD Dataset
- Metabolites - Metabolomic Dataset
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 1 years agofrom:b031307ed0. Checks:OK: 1 WARNING: 1. Indexed: no.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 03 2024 |
| R-4.5-linux | WARNING | Nov 03 2024 |
Exports:allbrancheschemical.dissimilarityclusters.detectiondiseasesMetenzymesMetfeaturesKODAMA.chem.simnameMetpathwaysMetpropertiesMetreadMetselectionMetsubstituentsMettaxonomyMettree.cuttingWMCSAwrite.clswrite.gctwrite.gmt
Dependencies:askpasscurlfingerprintherehttriteratorsitertoolsjsonliteKODAMAlatticeMatrixmimeminervaopensslpngR6rappdirsrcdkrcdklibsRcppRcppArmadilloRcppEigenRcppTOMLreticulaterJavarlangrprojrootRSpectraRtsnesysumapwithrXML
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Cut a Tree into Groups of Data | allbranches |
| Chemical dissimilarity. | chemical.dissimilarity |
| ChemRICH Dataset | ChemRICH |
| Detection of clusters. | clusters.detection |
| Metabolite-associated Diseases | diseasesMet |
| Metabolite-associated Enzymes | enzymesMet |
| Cluster features extraction | features |
| HFD Dataset | HFD |
| KODAMA chemical similarity. | KODAMA.chem.sim |
| Metabolomic Dataset | Metabolites |
| Name of metabolites | nameMet |
| Metabolic Pathways | pathwaysMet |
| Physical Proprieties of metabolites | propertiesMet |
| Metabolite Cards Reading | readMet |
| Metabolites selection | selectionMet |
| Metabolite substituents | substituentsMet |
| Metabolite Taxonomy | taxonomyMet |
| Optimal cluster number calculation. | tree.cutting |
| Weighted Metabolite Chemical Structural Analysis | WMCSA |
| Write a CLS file | write.cls |
| Write a GCT file | write.gct |
| Write a GMT file | write.gmt |
