BiocWorkflowTools

BiocWorkflowTools enables authors to work with R Markdown documents and convert them to LaTeX format for submission to the F1000Research Bioconductor Gateway while maintaining executable workflow compatibility with Bioconductor.

Key Features:

• R Markdown to LaTeX conversion: Provides functions to ease the transition between Rmarkdown and LaTeX documents when authoring a Bioconductor Workflow.
• Automated figure and reference handling: Reduces manual intervention previously required for floating figures, cross-references, literature references, and author affiliations during format conversion.
• Single-source workflow authoring: Enables authors to maintain one R Markdown source document that can serve both as an executable Bioconductor workflow and as a submission-ready LaTeX article for peer-reviewed publication.

Scientific Applications:

• Bioconductor Workflow publication: Supports creation of peer-reviewed, citable end-to-end data analysis workflows rooted in the Bioconductor ecosystem for the F1000Research platform.
• Executable workflow distribution: Facilitates deposition of workflows as executable documents on Bioconductor with benefits of regular code testing and easy updating.

Methodology:

Conversion between R Markdown and LaTeX formats using functions that handle document elements including floating figures, cross-references, literature references, and author affiliations.