ariadne: assembling relational information across the database network

ariadne is a multi-purpose R package that integrates relational knowledge from various biological databases. It provides tools to navigate resource graphs, find and visualise paths between features and link them across different omics by leveraging the resource graph hosted in the companion package ariadne.db.

Example applications:

• explore relations across omics using curated knowledge, fetched automatically and efficiently using SPARQL and parquet
• stratify microbes by BugSig and Gut Metabolic modules for functional or microbe-set enrichment analysis
• converge features from different taxonomies (NCBI, SILVA, OTT, etc.)

Usage

Installation instructions

In the future, we intend to submit ariadne to Bioconductor. For now, the package can be installed with:

remotes::install_github("Minotau-R/ariadne")

Code of Conduct

Please note that the ariadne project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms. Contributions are welcome in the form of feedback, issues and pull requests. You can find the contributor guidelines of the miaverse here.

Acknowledgements

ariadne results from the joint effort of the larger bioinformatics community. In particular, this software is related to the following packages:

• MultiFactor
• mia