Package: pubchem.bio 1.0.5

Corey Broeckling

pubchem.bio: Biologically Informed Metabolomic Libraries from 'PubChem'

All 'PubChem' compounds are downloaded to a local computer, but for each compound, only partial records are used. The data are organized into small files referenced by 'PubChem' CID. This package also contains functions to parse the biologically relevant compounds from all 'PubChem' compounds, using biological database sources, pathway presence, and taxonomic relationships. Taxonomy is used to generate a lowest common ancestor taxonomy ID (NCBI) for each biological metabolite, which then enables creation of taxonomically specific metabolome databases for any taxon.

Authors:Corey Broeckling [aut, cre]

pubchem.bio_1.0.5.tar.gz
pubchem.bio_1.0.5.tar.gz(r-4.7-any)pubchem.bio_1.0.5.tar.gz(r-4.6-any)
pubchem.bio_1.0.5.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
pubchem.bio/json (API)
NEWS

# Install 'pubchem.bio' in R:
install.packages('pubchem.bio', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))
Uses libs:
  • openjdk– OpenJDK Java runtime, using Hotspot JIT
Datasets:

On CRAN:

Conda:

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

openjdk

3.18 score 4 scripts 180 downloads 11 exports 109 dependencies

Last updated from:bb6c27d1a8. Checks:4 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK161
source / vignettesOK221
linux-release-x86_64OK163
wasm-releaseOK167

Exports:%>%build.cid.lcabuild.element.countbuild.primary.metabolomebuild.pubchem.biobuild.taxon.metabolomeexport.ComboundDbexport.msfinderexport.pubchem.bioexport.siriusget.pubchem.ftp

Dependencies:AnnotationFilterbase64encBHBiobaseBiocGenericsBiocParallelbitbit64bitopsblobbslibcachemChemmineRCHNOSZcliclueclustercodetoolsCompoundDbcpp11crosstalkcurldata.tableDBIdbplyrdigestdoParalleldplyrDTevaluatefarverfastmapfingerprintfontawesomeforeachformatRfsfutile.loggerfutile.optionsgenericsGenomicRangesggplot2gluegridExtragtablehighrhtmltoolshtmlwidgetsIRangesisobanditeratorsitertoolsjquerylibjsonliteknitrlabelinglambda.rlaterlazyevallifecyclemagrittrMASSmemoiseMetaboCoreUtilsmimeMsCoreUtilsotelpillarpkgconfigpngpromisesProtGenericspurrrR.methodsS3R.ooR.utilsR6rappdirsrcdkrcdklibsRColorBrewerRcppRCurlrJavarjsonrlangrmarkdownRSQLitersvgS4VectorsS7sassscalesSeqinfosnowSpectrastringistringrtibbletidyrtidyselecttinytexutf8vctrsviridisLitewithrxfunxml2yaml

pubchem.bio

Corey Broeckling

Rendered frompubchem.bio.vignette.Rmdusingknitr::rmarkdownon May 21 2026.

Last update: 2026-01-21
Started: 2025-08-28

Readme and manuals

Help Manual

Help pageTopics
build.cid.lcabuild.cid.lca
build.element.countbuild.element.count
build.primary.metabolomebuild.primary.metabolome
build.pubchem.biobuild.pubchem.bio
build.taxon.metabolomebuild.taxon.metabolome
cid.accurate.mass.rdacid.accurate.mass
cid.cas.rdacid.cas
cid.formula.rdacid.formula
cid.inchi.rdacid.inchi
cid.inchikey.rdacid.inchikey
cid.lca.rdacid.lca
cid.mesh.function.rdacid.mesh.function
cid.mesh.name.rdacid.mesh.name
cid.monoisotopic.mass.rdacid.monoisotopic
cid.monoisotopic.mass.rdacid.monoisotopic.mass
cid.parent.rdacid.parent
cid.pmid.rdacid.pmid
cid.pmid.ct.rdacid.pmid.ct
cid.preferred.rdacid.preferred
cid.pwid.rdacid.pwid
cid.sid.rdacid.sid
cid.smiles.rdacid.smiles
cid.synonym.rdacid.synonym
cid.taxid.rdacid.taxid
cid.title.rdacid.title
export.ComboundDbexport.ComboundDb
export.msfinderexport.msfinder
export.pubchem.bioexport.pubchem.bio
export.siriusexport.sirius
get.pubchem.ftpget.pubchem.ftp
pc.bio.subset.rdapc.bio.subset
pubchem.bio.rdapubchem.bio
sub.taxid.hierarchy.rdasub.taxid.hierarchy
taxid.hierarchy.rdataxid.hierarchy