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Streamlined Tidy Data Access to Open Targets Genetics GraphQL API 🔍

otargen is an open-source R package for easy data retrieval and analysis from Open Targets Genetics. It simplifies the analysis of human genetic evidence for gene-trait/disease associations within the R environment, enhancing your research with advanced data handling and visualization tools.

📢 otargen 1.1.5

In this new release, several frequently requested query functions from Open Targets’ GraphQL API have been added to expand the package’s functionality in accessing key data for drug target evaluation. Additionally, multiple technical bugs have been fixed to improve the efficiency of data retrieval from previous query functions. The newly added query functions include:

  • chemblQuery(): Queries the Open Targets GraphQL API to retrieve ChEMBL data for a specified gene and disease, including evidence from the ChEMBL datasource.

▶️ These data are key in evaluating the tractability of a target.

  • clinvarQuery(): Queries the Open Targets GraphQL API to retrieve ClinVar data for a specified gene and disease, including evidence from the NCBI datasource.

▶️ These data are key to evaluating the target’s mechanism of action (MoA) and disease biology.

  • knownDrugsQuery(): Queries the Open Targets GraphQL API to retrieve known drug data for a specified gene.

▶️ These data are key to evaluating the competitive landscape of a target.

  • mousePhenotypesQuery(): Queries the Open Targets GraphQL API to retrieve mouse phenotypes data for a specified gene.

▶️ These data are key in target validation.

  • compGenomicsQuery(): Queries the Open Targets GraphQL API to retrieve comparative genomics data for a specified gene.

▶️ These data are key in evaluating the safety of a target.

Installation

Get started with otargen from CRAN:

install.packages("otargen")

Or install the latest development version from GitHub:

if (!require("devtools")) install.packages("devtools")
devtools::install_github("https://github.com/amirfeizi/otargen.git")

Citing otargen is important for us 🙋‍

Please cite otargen if you use it in your research 🙏. Bioinformatics.

📢 otargenpy is available for Python users 🐍
Install via pip: pip install otargenpy

Check out the repository here: otargenpy on GitHub. otargenpy has all the capabilities of otargen. We encourage you to try it out and provide us with feedback!

Key Features

🚀 Effortless Data Retrieval: Easily access and transform complex GraphQL queries.

📈 Insightful Visualizations: Clearly visualize complex datasets with intuitive plots.

📖 Comprehensive Documentation: Well-documented functions for easy integration.

👨‍💻 Regular Updates: Stay updated with new features and improvements.

Community and Contributions

Join the otargen community on GitHub and contribute to its growth. We welcome bug reports, feature suggestions, and code contributions.