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MetaDBparse

Parsing metabolomics databases with publically available resources

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Version

Install

install.packages('MetaDBparse')

Monthly Downloads

11

Version

2.0.0

License

Apache License 2.0

Maintainer

Joanna Wolthuis

Last Published

May 3rd, 2021

Functions in MetaDBparse (2.0.0)

build.METACYC

Build METACYC
build.T3DB

Build T3DB
build.DIMEDB

Build DIMEDB
build.METABOLIGHTS

Build METABOLIGHTS DB
buildExtDB

Build external database using a given base database
build.MCDB

Build MCDB
build.VMH

Build VMH
buildBaseDB

Build the base database
doAdduct

Generate adduct for given structure
doBT

Run Biotransformer on SMILES.
build.ANPDB

Build ANPDB
lmdb

LMDB
pubChemInfo

Find additional info on a PubChem ID.
writeDB

Write table to SQLite database
build.REACTOME

Build REACTOME db
smiles.to.iatom

Get iatom containers from SMILES
build.PHENOLEXPLORER

Build PHENOL EXPLORER DB
removeDB

Remove database
build.ECMDB

Build ECMDB
build.PAMDB

Build PAMDB
build.PHARMGKB

Build PharmGKB
openBaseDB

Create/open and prepare SQLite database
build.FOODB

Build FOODB
build.YMDB

Build YMDB
build.mVOC

Build mVOC db
downloadBT

Download biotransformer jar file.
doIsotopes

Generate isotopes for given formula
build.LIPIDMAPS

Build LIPID MAPS
build.LMDB

Build LMDB
searchFormula

Find matches based on molecular formula
searchFormulaWeb

Find web hits for a molecular formula
countAdductRuleMatches

Check which structures are OK according to given adduct rules
build.STOFF

Build STOFF db
iatom.to.charge

Get formal charge from iatomcontainer
build.MASSBANK

Build MASSBANK DB
build.SMPDB

Build SMPDB
cleanDB

Uniformize database and remove invalid formulas/SMILES
build.MACONDA

Build MACONDA
getPredicted

Get predicted formulas and adducts from m/z value
checkAdductRule

Check for combined adduct rules
build.RESPECT

Build RESPECT
chemspiderInfo

Find more info through ChemSpider.
searchCMMR

Search CMMR
build.WIKIDATA

Build Wikidata
filterFormula

Apply seven golden rules to a vector of formulas
iatom.to.smiles

Get SMILES from iatom container
revertAdduct

Break formula apart into adduct and main formula
searchMZ

Find matches for m/z value in given database
iatom.to.formula

Get molecular formula from iatomcontainer
removeFailedStructures

Remove structures where isotope generation failed.
build.RMDB

Build RMDB (deprecated)
sdfStream.joanna

Adjusted sdfStream version for databases that store their compounds in SDF format
searchMZonline

Find m/z matches with CMMR, ChemSpider or PubChem
build.WIKIPATHWAYS

Build WikiPathways
is.empty

Is this item 'empty'?
getFormula

Find possible formulas for a given m/z
showAllBase

Show all compounds in base db
isotopes

Weights of all isotopes of all elements used
searchRev

Reverse searching
build.BMDB

Build BMDB
adducts

Adduct table
build.BLOODEXPOSOME

Build BLOOD EXPOSOME DB
build.EXPOSOMEEXPLORER

Build EXPOSOME EXPLORER
build.CHEBI

Build CHEBI
build.DRUGBANK

Build DRUGBANK
adduct_rules

Adduct rule table
build.HMDB

Build HMDB
build.KEGG

Build KEGG