BOLDconnectR

An R package that supports programmatic interaction with the Barcode of Life Data System’s Workbench and Portal.

Overview
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Supporting Self-Directed Analysis

BOLDconnectR is a package composed of 6 core functions, which are designed to streamline the analysis and curation of data on BOLD. The provided tools allow users to effortlessly retrieve, analyze, and visualize DNA barcode data. Each function is engineered to provide maximum flexibility, supporting the development of customized workflows.

Core Functions

bold.public_search

Search public BOLD data by taxonomy, geography, or dataset codes. Filter results and retrieve process and sample IDs.

bold.fetch

Retrieve public and private user data in bulk, formatted in Barcode Core Data Model (BCDM), with customizable filters and output.

bold.analyze.tree

Generate Neighbor-Joining trees from sequence alignments, with options for distance matrix calculations and Newick format export.

bold.export

Export sequence data to FASTA or CSV/TSV formats with customizable sequence naming, preserving BCDM format.

bold.analyze.diversity

Calculate species richness and diversity indexes, visualizing results in plots and matrices for detailed analysis.

bold.analyze.map

Map geographic data from BOLD, displaying data points on global or regional maps in GIS-compatible formats.

Learn more

BOLDconnectR is easy to install and use, with comprehensive documentation and examples to help you get started. Explore the package's capabilities and see how it can transform your research.

Capabilities

Direct API Access: Effortlessly retrieve species identification, taxonomy, and sequence data from BOLD without writing any new code.
Integration with Popular Tools BOLDconnectR supports the integration of BOLD data with other R packages, enabling comprehensive analysis and visualization.
Custom Workflows Users can design tailored workflows for specific research needs, enhancing the efficiency and scope of their data analysis.

Join the BOLDconnectR Community

Connect with other researchers using BOLDconnectR and contribute to its development. Share your workflows, scripts, and findings to help improve this tool for the broader scientific community.