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PubChemR (version 3.0.0)

Interface to the 'PubChem' Database for Chemical Data Retrieval

Description

Provides an interface to the 'PubChem' database via the PUG REST and 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.

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Install

install.packages('PubChemR')

Monthly Downloads

382

Version

3.0.0

License

GPL (>= 2)

Issues

Pull Requests

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Repository

https://github.com/selcukorkmaz/PubChemR

Homepage

https://selcukorkmaz.github.io/pubchemr-tutorial/

Maintainer

Selcuk Korkmaz

Last Published

March 7th, 2026

Functions in PubChemR (3.0.0)

Retrieve Substances from PubChem

Retrieve Synonyms from PubChem

Retrieve Substance IDs (SIDs) from PubChem

Check Whether Queries Returned Hits

Retrieve Compound Properties from PubChem

pc_capabilities

Inspect Next-Generation Workflow Capabilities

Batch-Orchestrate PubChem Workflows

pc_lifecycle_policy

Versioning and Deprecation Policy

Retrieve Data from PubChem PUG REST API

pc_assay_activity_long

Convert PubChem Assay Summary to Long Activity Table

Retrieve PUG View Data from PubChem

pc_example_assaysummary_payload

Example Assay Summary Payload for Next-Generation Workflows

pc_cross_domain_join

Join Compound, Substance, Assay, and Target Tables

Retrieve/Save SDF Data from PubChem

pc_activity_outcome_map

Harmonize Activity Outcome Labels

pc_model_matrix

Convert Feature Tables to Model Matrix Form

pc_feature_table

Build a Modeling-Ready Feature Table

Collect Results From an Async PubChem Query

pc_identifier_map

Map Identifiers via the Next-Generation API

Normalize an HTTP Response Into a Typed PubChem Result

Apply a Predefined Execution Profile

Poll an Asynchronous PubChem ListKey

Submit an Asynchronous PubChem Query

Cache Diagnostics for PubChemR

Clear PubChemR Request Cache

pc_resume_batch

Resume a Checkpointed Batch Workflow

List Available Section/Subsections

Getter function for 'Synonyms'

Query Substance Records via the Next-Generation API

Benchmark Chunked PubChem Workflows

pc_activity_matrix

Build an Assay Activity Matrix

Query Compound Records via the Next-Generation API

pc_benchmark_harness

Benchmark Harness for Scale Scenarios

Retrieve Information for Requested Instances

Query Assay Records via the Next-Generation API

pc_similarity_search

Similarity-Driven Identifier Search

Configure PubChemR Next-Gen API Defaults

pc_sdq_bioactivity

Retrieve Full Biological Test Results from PubChem SDQ

Extract Sections from Pug View Request

Convert PubChem Tables to rcdk Molecules

Unified Transport Layer for PubChem Requests

pc_export_model_data

Export Model-Ready Data

pc_example_feature_table

Example Feature Table for Next-Generation Modeling Workflows

pc_to_chemminer

Convert PubChem Tables to ChemmineR SDF Objects

Query Compound Properties via the Next-Generation API

Retrieve Raw Data from PUG REST Object

Retrieve Information from PubChem Instances

Retrieve Function Inputs

Assay, Compound, and Substance Identifiers

PubChemR-classes

PubChemInstanceList and PubChemInstance Classes

get_all_sources

Retrieve All Sources from PubChem

Retrieve Compound IDs (CIDs) from PubChem

Retrieve Assay IDs (AIDs) from PubChem

get_biological_test_results

Retrieve "Biological Test Results" Section from PubChem Contents

Retrieve Compounds from PubChem

Retrieve Assays from PubChem

Download Content from PubChem and Save to a File

PugView-classes

Classes for Pug View Request