Skip to content


Switch branches/tags

Latest commit

…kdown and Quarto from (#48)

* Update

I added references to quarto: It is a open source framework following a similar style as R Markdown, however it can easily implement the execution of R, Python, Julia and OBJ. Furthermore, its writing is not limited to markdown files, as it can also render Jupyter Notebooks to scientific articles, presentations, and interactive websites. Besides adding quarto to this collection I added two tutorials (one for academic writing in R Markdown interconnected with Notion & Zotero, and one for writing in Quarto) from my own blog.

* Update

adapted alphabetical order

* Update

Added Quarto only once, and added descriptions to all my entries

* Update

* Update

Git stats


Failed to load latest commit information.

Awesome Scientific Writing Awesome

Scientific writing can extend beyond LaTeX, made possible by formats, such as Markdown (and its many flavours), reStructuredText and Jupyter notebooks.

🔖 means ability to seamlessly cite references.

🔗 means ability to cross-reference figures and sections within the document.


Word Processors

  • Atom - Popular IDE with Markdown support.
  • Marktext - Markdown text editor.
  • R Studio - IDE for R.
    • bookdown - R package to facilitate writing books and long-form articles, reports with R Markdown 🔖 🔗.
    • R Markdown - R package to write R next to Markdown 🔖 🔗.
  • Vim - Command line text editor.
    • fzf-bibtex - BibTeX source with Vim integration which uses fzf (a fuzzy finder implemented in Go).
    • vim-pandoc - Pandoc integration and utilities for Vim.
    • vim-pandoc-syntax - Pandoc syntax highlighting for Vim.
  • Visual Studio Code - Popular IDE with Markdown support.
    • Markdown All in One - Extension for enhanced Markdown support in VSCode, such as preview and auto completion to name a few.
  • Zettlr - Markdown editor which integrates CSL, BibLaTeX, Pandoc and many other tools 🔖 🔗.


Reference managers to generate citations, BibTeX, and BibLaTeX files.


Drawing illustrations themselves has driven many a scientist mad. Fortunately, there are formal languages with which one can create beautiful graphics.

  • - Open source, online, desktop and container deployable diagramming software.
  • graphviz - Visualization software for graphs and networks which uses a domain-specific DOT language.
  • Mermaid Live Editor - Define simple diagrams instead of drawing them.
  • Vega Lite - Define charts and more complex diagrams.
  • PlantUML - Define UML diagrams instead of drawing them.

Converters and Filters

Supplementary files and tools.

  • Cicero - Python package which renders HTML presentations from Markdown source using remark or reveal.js 🔗.
  • docutils - Python package which can convert reStructuredText into various formats and provides command-line tools to do it 🔗.
  • Jupyter Book - A static site generator which converts a collection of CommonMark, MyST markdown and Jupyter notebooks into a HTML website.
  • MyST - Markedly Structured Text, a superset of CommonMark markdown with reStructuredText like features.
  • nbconvert - Convert Jupyter notebooks into reveal.js presentations, PDF, HTML, Markdown, reStructuredText and more.
  • pandoc - Haskell library for converting from one markup format to another, and a command-line tool that uses this library 🔖 🔗.
    • Academic Markdown - Python wrapper over Pandoc with specialized extensions to parse certain elements, making it a superset of Pandoc Markdown flavour 🔖 🔗.
    • Pandoc filters - List of addons to pandoc which implement extra features such as citations and cross-references.
    • Panflute - Pythonic alternative to John MacFarlane's pandocfilters.
  • Quarto - Compile R Markdown, and Jupyter Notebooks to PDFs, Slides and Websites. Supports R, Python, and Julia 🔖 🔗.

Spell Checking and Linting


Reusable minimalist examples.


  • Pandoc Markdown-LaTeX Boilerplate - Demonstrate how to integrate Pandoc with an existing LaTeX template which requires some boilerplate code (i.e. LaTeX preamble), thus avoiding the latexmk dependency.
  • scientific-markdown - Example for use of Markdown for scientific publications using Pandoc and latexmk.
  • Steve's R Markdown Templates - Academic manuscript, memos, Beamer presentation, syllabus and CV.


  • pandoc-starter - Templates for articles, Beamer presentations etc. using Markdown files and Makefiles for getting started with Pandoc.
  • slides - Demo for generating reveal.js presentations using Pandoc.



How to generate articles and presentations for scientific purposes.

Other Lists


Contributions welcome! Read the contribution guidelines first.