Provides parsing functionality for over 30 metabolomics databases, with most available without having to create an account on given websites. Once parsed, calculates given adducts and isotope patterns and inserts into one big database which can be used to annotate unknown m/z values. Furthermore, formulas can be predicted for a given m/z, and these can be matched to ChemSpider or PubChem for further annotation. Current databases available: HMDB, ChEBI, LMDB, RMDB, BMDB, MCDB, ECMDB, Wikidata, mVOC, VMH, T3DB, Exposome Explorer, FooDB, MetaCyc (requires account), DrugBank (requires account), ReSPECT, MaConDa, Blood Exposome DB, KEGG, SMPDB, LIPID MAPS, MetaboLights, DimeDB, Phenol Explorer, MassBank, YMDB, PAMDB, NANPDB and STOFF. Featured in the 'MetaboShiny' package (Wolthuis, J. (2019) <doi:10.1101/734236>).
| Version: | 1.0.0 |
| Depends: | R (≥ 2.10), rvest, RCurl, XML, SPARQL |
| Imports: | methods, pacman, rcdk, rJava, parallel, pbapply, enviPat, data.table, RSQLite, DBI, gsubfn, utils, base, stringr, WikidataQueryServiceR, webchem, openxlsx, jsonlite, R.utils, KEGGREST, zip, ChemmineR, xml2, stringi, reshape2, Hmisc, httr, RJSONIO, readxl, cmmr, progress, Rdisop, rlist |
| Published: | 2020-09-09 |
| Author: | Joanna Wolthuis |
| Maintainer: | Joanna Wolthuis <J.C.Wolthuis-2 at umcutrecht.nl> |
| License: | Apache License 2.0 |
| NeedsCompilation: | no |
| Materials: | README |
| CRAN checks: | MetaDBparse results |
| Reference manual: | MetaDBparse.pdf |
| Package source: | MetaDBparse_1.0.0.tar.gz |
| Windows binaries: | r-devel: MetaDBparse_1.0.0.zip, r-release: MetaDBparse_1.0.0.zip, r-oldrel: MetaDBparse_1.0.0.zip |
| macOS binaries: | r-release: not available, r-oldrel: not available |
Please use the canonical form https://CRAN.R-project.org/package=MetaDBparse to link to this page.