Package: PubChemR 2.1.2

Selcuk Korkmaz

PubChemR: Interface to the 'PubChem' Database for Chemical Data Retrieval

Provides an interface to the 'PubChem' database via the PUG REST <https://pubchem.ncbi.nlm.nih.gov/docs/pug-rest> and PUG View <https://pubchem.ncbi.nlm.nih.gov/docs/pug-view> services. This package allows users to automatically access chemical and biological data from 'PubChem', including compounds, substances, assays, and various other data types. Functions are available to retrieve data in different formats, perform searches, and access detailed annotations.

Authors:Selcuk Korkmaz [aut, cre], Bilge Eren Yamasan [aut], Dincer Goksuluk [aut]

PubChemR_2.1.2.tar.gz
PubChemR_2.1.2.zip(r-4.5)PubChemR_2.1.2.zip(r-4.4)PubChemR_2.1.2.zip(r-4.3)
PubChemR_2.1.2.tgz(r-4.5-any)PubChemR_2.1.2.tgz(r-4.4-any)PubChemR_2.1.2.tgz(r-4.3-any)
PubChemR_2.1.2.tar.gz(r-4.5-noble)PubChemR_2.1.2.tar.gz(r-4.4-noble)
PubChemR_2.1.2.tgz(r-4.4-emscripten)PubChemR_2.1.2.tgz(r-4.3-emscripten)
PubChemR.pdf |PubChemR.html✨
PubChemR/json (API)

# Install 'PubChemR' in R:

install.packages('PubChemR', repos = c('https://selcukorkmaz.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/selcukorkmaz/pubchemr/issues

On CRAN:

5.62 score 2 stars 23 scripts 472 downloads 24 exports 51 dependencies

Last updated 5 months agofrom:37a41a0293. Checks:1 OK, 5 ERROR, 2 WARNING. Indexed: yes.

Target	Result	Latest binary
Doc / Vignettes	OK	Mar 01 2025
R-4.5-win	ERROR	Mar 01 2025
R-4.5-mac	WARNING	Mar 01 2025
R-4.5-linux	ERROR	Mar 01 2025
R-4.4-win	WARNING	Mar 01 2025
R-4.4-mac	ERROR	Mar 01 2025
R-4.3-win	ERROR	Mar 01 2025
R-4.3-mac	ERROR	Mar 01 2025

Exports:AIDs CIDs download get_aids get_all_sources get_assays get_cids get_compounds get_properties get_pug_rest get_pug_view get_sdf get_sids get_substances get_synonyms instance property_map pubChemData request_args retrieve section sectionList SIDs synonyms

Dependencies:askpass bitops brio callr cli cpp11 crayon curl desc diffobj digest dplyr evaluate fansi fs generics glue httr jsonlite lifecycle magick magrittr mime openssl pillar pkgbuild pkgconfig pkgload png praise processx ps purrr R6 Rcpp RCurl RJSONIO rlang rprojroot rsvg stringi stringr sys testthat tibble tidyr tidyselect utf8 vctrs waldo withr

Accessing and Exploring Chemical Data with PubChemR: A Guide to PUG REST Service

Selcuk Korkmaz, Bilge Eren Korkmaz, Dincer Goksuluk

Rendered fromExploring_Chemical_Data_with_PubChemR.Rmdusingknitr::rmarkdownon Mar 01 2025.

Last update: 2024-10-02
Started: 2023-12-11

Enhancing Chemical Data Access with PubChemR: A Guide to Utilizing PUG View Service

Selcuk Korkmaz, Bilge Eren Yamasan, Dincer Goksuluk

Rendered fromEnhancing_Chemical_Data_Access_with_PubChemR.Rmdusingknitr::rmarkdownon Mar 01 2025.

Last update: 2024-09-27
Started: 2023-12-11

Working with PubChemR to Access Chemical Data

Selcuk Korkmaz, Bilge Eren Yamasan, Dincer Goksuluk

Rendered fromWorking_with_PubChemR_to_Access_Chemical_Data.Rmdusingknitr::rmarkdownon Mar 01 2025.

Last update: 2024-07-12
Started: 2023-11-06

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Assay, Compound, and Substance Identifiers	AIDs AIDs-SIDs-CIDs AIDs.PubChemInstance_AIDs CIDs CIDs.PubChemInstance_CIDs SIDs SIDs.PubChemInstance_SIDs
Download Content from PubChem and Save to a File	download
Retrieve Assay IDs (AIDs) from PubChem	get_aids
Retrieve All Sources from PubChem	get_all_sources
Retrieve Assays from PubChem	get_assays
Retrieve Compound IDs (CIDs) from PubChem	get_cids
Retrieve Compounds from PubChem	get_compounds
Retrieve Compound Properties from PubChem	get_properties property_map
Retrieve Data from PubChem PUG REST API	get_pug_rest
Retrieve PUG View Data from PubChem	get_pug_view
Retrieve/Save SDF Data from PubChem	get_sdf
Retrieve Substance IDs (SIDs) from PubChem	get_sids
Retrieve Substances from PubChem	get_substances
Retrieve Synonyms from PubChem	get_synonyms
Retrieve Information for Requested Instances	instance instance.PubChemInstanceList
Retrieve Raw Data from PUG REST Object	pubChemData pubChemData.PugRestInstance
'PubChemInstanceList' and 'PubChemInstance' Classes	PubChemR-classes
Classes for Pug View Request	PugView-classes
Retrieve Function Inputs	request_args
Retrieve Information from PubChem Instances	retrieve retrieve.PC_Substance retrieve.PubChemInstance retrieve.PubChemInstanceList retrieve.PugViewInstance retrieve.PugViewSection
Extract Sections from Pug View Request	section section.PugViewInstance section.PugViewSection section.PugViewSectionList
List Available Section/Subsections	sectionList sectionList.PugViewInstance sectionList.PugViewSection sectionList.PugViewSectionList
Getter function for 'Synonyms'	synonyms synonyms.PubChemInstance_Synonyms