Word Processors

• Marktext (⭐52k) - Markdown text editor.

Spell Checking and Linting

• proselint (⭐4.5k) - Linter for prose.

Tutorials / Books

• 3 frameworks into one — Write your next paper with R Studio! - Article provides an overview to a workflow that combines R Markdown (bookdown), Zotero (literature management), and Notion (note taking on research papers) to write academic papers.

• Heads up! Quarto is here to stay. Immediately combine R & Python in your next document - Summary of the capabilities of Quarto, why to use it, and how it compares to R Markdown. Also contains tips for M1 Mac users on how to fix a common problem with reticulate.

Illustrations

• app.diagrams.net - Open source, online, desktop and container deployable diagramming software named draw.io.

Spell Checking and Linting

• LanguageCheck (⭐109) - Analyses scientific LaTeX papers, suggesting improvements from a list of common mistakes/ambiguities, tense consistency, a vs. an, spell check, and paragraph topic sentences.

Tutorials / Books

• Scott Selisker - Plain Text Workflow for Academic Writing with Atom.

Converters and Filters

• Quarto - Compile R Markdown, and Jupyter Notebooks to PDFs, Slides and Websites. Supports R, Python, and Julia 🔖 🔗.

Tutorials / Books

• Write your dissertation in RMarkdown - Step-by-step guide on creating a complex pdf document, including text, figures, references, images, formatting, and more.

Other Lists / Books

• Awesome Jupyter (⭐4.5k)

• Awesome LaTeX (⭐1.6k)

• Awesome Markdown (⭐903)

• Delightful Open Science

Converters and Filters

• 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.

Word Processors

• Visual Studio Code - Popular IDE with Markdown support.
  • Markdown All in One (⭐3.1k) - Extension for enhanced Markdown support in VSCode, such as preview and auto completion to name a few.
  • Markdown Preview Enhanced (⭐4.3k) - Pandoc integration and utilities.

Converters and Filters

• Cicero - Python package which renders HTML presentations from Markdown source using remark or reveal.js 🔗.

Spell Checking and Linting

• restructuredtext-lint (⭐180) - reStructuredText linter.

• textlint - Pluggable linting tool for text and Markdown.

Tutorials / Books

• Katrin Leinweber's Ph.D. thesis (⭐50) - Automated work flow involving several tools, but primarily Pandoc, latexmk and Academic Markdown.

Bibliography

• ZoteroBib - Online bibliography reference manager.

Templates / Books

• Eisvogel (⭐6.9k) - Clean academic pandoc LaTeX template.

Word Processors

• Vim - Command line text editor.
  • fzf-bibtex (⭐133) - BibTeX source with Vim integration which uses fzf (a fuzzy finder implemented in Go).
  • vim-pandoc (⭐967) - Pandoc integration and utilities for Vim.
  • vim-pandoc-syntax (⭐424) - Pandoc syntax highlighting for Vim.

Bibliography

• Citation Style Language (CSL) styles - Crowdsourced repository with over 9000 free CSL citation styles and an online editor to create new ones.

• Zotero - FOSS tool to collect, organize, cite, and share research.
  • Better BibTeX for Zotero - Enhanced BibTeX / BibLaTeX integration for Zotero.
  • ZotFile for Zotero - Enhanced PDF file management for Zotero.

Illustrations

• graphviz - Visualization software for graphs and networks which uses a domain-specific DOT language.

Converters and Filters

• docutils - Python package which can convert reStructuredText into various formats and provides command-line tools to do it 🔗.

• 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 (⭐354) - Python wrapper over Pandoc with specialized extensions to parse certain elements, making it a superset of Pandoc Markdown flavour 🔖 🔗.
  • Pandoc filters (⭐40k) - List of addons to pandoc which implement extra features such as citations and cross-references.
  • Panflute - Pythonic alternative to John MacFarlane's pandocfilters.

Spell Checking and Linting

• GNU Aspell - Command line spell checker.

• Hunspell - Command line spell checker.

• Markdown lint tool (⭐2k) - Markdown linter.

• remarklint (⭐1k) - Markdown linter.

Word Processors

• R Studio (⭐4.9k) - IDE for R.
  • bookdown (⭐4k) - R package to facilitate writing books and long-form articles, reports with R Markdown 🔖 🔗.
  • R Markdown - R package to write R next to Markdown 🔖 🔗.

• Zettlr - Markdown editor which integrates CSL, BibLaTeX, Pandoc and many other tools 🔖 🔗.

Bibliography

• JabRef - Open source bibliography reference manager.

Illustrations

• 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.

Templates / Articles

• Pandoc Markdown-LaTeX Boilerplate (⭐101) - 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 (⭐54) - Example for use of Markdown for scientific publications using Pandoc and latexmk.

• Steve's R Markdown Templates (⭐927) - Academic manuscript, memos, Beamer presentation, syllabus and CV.

Templates / Presentations

• pandoc-starter (⭐539) - Templates for articles, Beamer presentations etc. using Markdown files and Makefiles for getting started with Pandoc.

• slides (⭐3) - Demo for generating reveal.js presentations using Pandoc.

Templates / Books

• bookdown-demo (⭐528) - Minimal example of a book based on R Markdown and bookdown.

• Template for writing a PhD thesis in Markdown (⭐1.3k) - Clean organization of files to provide a framework for writing a PhD thesis in mostly Markdown with a little bit of LaTeX, and compiled with Pandoc.

Tutorials / Books

• Book on Riemann solvers (⭐282) - This example uses a custom nbconvert template and shows how to store your notebooks with no output (for version control) while automatically executing them before running bookbook, so that PDF and HTML versions include the output.

• Dennis Tenen and Grant Wythoff - Sustainable Authorship in Plain Text using Pandoc and Markdown.

• Teaching and learning with Jupyter (⭐458) - Book written in R Markdown, bookdown and also rendered as HTML, PDF and EPUB.

• Writing scientific papers for ACPD using Emacs Org-mode - Detailed tutorial on authoring a paper by seamlessly integrating with LaTeX commands within Org-mode.

Spell Checking and Linting

• LanguageTool - Open source grammar, style and spell Checker.

• textidote - Spelling, grammar and style checking on LaTeX documents.

• Vale (⭐5.1k) - Free, open-source linter for prose built with speed and extensibility in mind.

• write-good (⭐5k) - Naive linter for English prose.