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pubchem.bio  

Biologically Informed Metabolomic Libraries from 'PubChem'
View on CRAN: Click here


Download and install pubchem.bio package within the R console
Install from CRAN:
install.packages("pubchem.bio")

Install from Github:
library("remotes")
install_github("cran/pubchem.bio")

Install by package version:
library("remotes")
install_version("pubchem.bio", "1.0.5")



Attach the package and use:
library("pubchem.bio")
Maintained by
Corey Broeckling
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2025-08-28
Latest Update: 2025-08-28
Description:
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.
How to cite:
Corey Broeckling (2025). pubchem.bio: Biologically Informed Metabolomic Libraries from 'PubChem'. R package version 1.0.5, https://cran.r-project.org/web/packages/pubchem.bio. Accessed 11 Mar. 2026.
Previous versions and publish date:
1.0.0 (2025-08-28 09:40), 1.0.1 (2025-09-01 00:20), 1.0.3 (2025-12-12 17:40)
Other packages that cited pubchem.bio R package
View pubchem.bio citation profile
Other R packages that pubchem.bio depends, imports, suggests or enhances
Complete documentation for pubchem.bio
Functions, R codes and Examples using the pubchem.bio R package
Full pubchem.bio package functions and examples
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