Question 1

How to set up a scientific writing workflow with Markdown and Pandoc?

Accepted Answer

Start with a Markdown editor like VS Code with extensions, use Zotero for reference management with Better BibTeX, and apply Pandoc with templates like Eisvogel for PDF conversion, as suggested in the Tutorials and Templates sections.

Question 2

What's the best Markdown editor for academic citations?

Accepted Answer

Zettlr is highlighted for its built-in citation support with CSL and BibLaTeX, while VS Code extensions like Markdown All in One offer similar features, as indicated by the :bookmark: icon in the Word Processors list.

Question 3

Quarto vs R Markdown for scientific papers?

Accepted Answer

Quarto is more versatile, supporting multiple languages like Python and R in a single document, while R Markdown is tightly integrated with R for statistical analysis; Quarto is better for cross-language projects, as noted in the Converters section and tutorials.

Question 4

How to convert Jupyter notebooks to PDF with citations?

Accepted Answer

Use nbconvert for basic conversion or Quarto for enhanced support with citations, and integrate with Pandoc filters for reference handling, as detailed in the Converters and Filters section of the README.

Question 5

Is there a tool for spell-checking LaTeX documents in this list?

Accepted Answer

Yes, textidote is specifically listed for LaTeX documents, offering grammar and style checks, while tools like Vale can be adapted for plain-text alternatives, as covered in the Spell Checking and Linting section.

Question 6

What are the alternatives to LaTeX for thesis writing?

Accepted Answer

Markdown-based workflows with Pandoc and templates like the PhD thesis template provide LaTeX-like output without coding, using tools from the Templates section for structure and formatting.

Scientific Writing

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