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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.
| Version: | 1.0.0 |
| Depends: | R (≥ 3.5.0) |
| Imports: | foreach, doParallel, R.utils, data.table, dplyr, rcdk, stringr |
| Suggests: | utils, knitr, rmarkdown, formatR |
| Published: | 2025-08-28 |
| DOI: | 10.32614/CRAN.package.pubchem.bio |
| Author: | Corey Broeckling [aut, cre] |
| Maintainer: | Corey Broeckling <cbroeckl at colostate.edu> |
| License: | GPL-3 |
| NeedsCompilation: | no |
| Materials: | NEWS |
| CRAN checks: | pubchem.bio results |
| Reference manual: | pubchem.bio.html , pubchem.bio.pdf |
| Vignettes: |
pubchem.bio (source, R code) |
| Package source: | pubchem.bio_1.0.0.tar.gz |
| Windows binaries: | r-devel: pubchem.bio_1.0.0.zip, r-release: not available, r-oldrel: pubchem.bio_1.0.0.zip |
| macOS binaries: | r-release (arm64): not available, r-oldrel (arm64): not available, r-release (x86_64): pubchem.bio_1.0.0.tgz, r-oldrel (x86_64): pubchem.bio_1.0.0.tgz |
Please use the canonical form https://CRAN.R-project.org/package=pubchem.bio to link to this page.
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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