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
- Bibliography
- Illustrations
- Converters and Filters
- Spell Checking and Linting
- Templates
- Tutorials
- Other Lists
- 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 :bookmark: :link:.
- 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.
- Markdown Preview Enhanced - Pandoc integration and utilities.
- Zettlr - Markdown editor which integrates CSL, BibLaTeX, Pandoc and many other tools :bookmark: :link:.
Reference managers to generate citations, BibTeX, and BibLaTeX files.
- Citation Style Language (CSL) styles - Crowdsourced repository with over 9000 free CSL citation styles and an online editor to create new ones.
- JabRef - Open source bibliography reference manager.
- 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.
- ZoteroBib - Online bibliography reference manager.
Drawing illustrations themselves has driven many a scientist mad. Fortunately, there are formal languages with which one can create beautiful graphics.
- app.diagrams.net - Open source, online, desktop and container deployable diagramming software named draw.io.
- 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.
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 🔖 🔗.
- GNU Aspell - Command line spell checker.
- Hunspell - Command line spell checker.
- LanguageTool - Open source grammar, style and spell Checker.
- LanguageCheck - Analyses scientific LaTeX papers, suggesting improvements from a list of common mistakes/ambiguities, tense consistency, a vs. an, spell check, and paragraph topic sentences.
- Markdown lint tool - Markdown linter.
- proselint - Linter for prose.
- remarklint - Markdown linter.
- restructuredtext-lint - reStructuredText linter.
- textlint - Pluggable linting tool for text and Markdown.
- textidote - Spelling, grammar and style checking on LaTeX documents.
- Vale - Free, open-source linter for prose built with speed and extensibility in mind.
- write-good - Naive linter for English prose.
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.
- bookdown-demo - Minimal example of a book based on R Markdown and bookdown.
- Eisvogel - Clean academic pandoc LaTeX template.
- Template for writing a PhD thesis in Markdown - 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.
How to generate articles and presentations for scientific purposes.
- 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.
- Book on Riemann solvers - 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 runningbookbook
, so that PDF and HTML versions include the output. - Dennis Tenen and Grant Wythoff - Sustainable Authorship in Plain Text using Pandoc and Markdown.
- 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.
- Katrin Leinweber's Ph.D.
thesis - Automated
work flow involving several tools, but primarily Pandoc,
latexmk
and Academic Markdown. - Scott Selisker - Plain Text Workflow for Academic Writing with Atom.
- Teaching and learning with Jupyter - Book written in R Markdown, bookdown and also rendered as HTML, PDF and EPUB.
- Write your dissertation in RMarkdown - Step-by-step guide on creating a complex pdf document, including text, figures, references, images, formatting, and more.
- Writing scientific papers for ACPD using Emacs Org-mode - Detailed tutorial on authoring a paper by seamlessly integrating with LaTeX commands within Org-mode.
Contributions welcome! Read the contribution guidelines first.