rrwrite-plan-manuscript

To generate a manuscript outline from a research repository, you provide the repository path and target journal. The system analyzes project structure, maps code and data files to sections, and outputs a structured outline file.

Yes, you can adapt manuscript outlines to specific journal guidelines like Nature or PLOS. The system adjusts section ordering, formatting, and word limit guidance based on the selected publication template.

To link code, data, and notebooks to manuscript sections automatically, the system analyzes the repository structure. It maps files like scripts, data, and documentation directly to standard manuscript sections.

The best way to ensure manuscript drafts align with journal word limits is using automated outline generation. The system provides section word targets and validation-ready workflow updates to track progress.

Yes, the manuscript outline planner works with Bioinformatics journal templates. It supports adapting outlines to Bioinformatics, Nature Methods, and PLOS Computational Biology formatting and section ordering requirements.

The manuscript outline planner produces an output file named outline.md in the target directory. This file contains section details, word targets, evidence files, and a validation-ready workflow update.