Awesome Scientific Writing 
Scientific writing can extend beyond LaTeX, made possible by formats,
such as
Markdown (and its many flavours),
reStructuredText and
Jupyter notebooks.
:bookmark: means ability to seamlessly cite references.
:link: means ability to cross-reference figures and sections within the
document.
Contents
Word Processors
- Marktext - Markdown text editor.
- R Studio - IDE for R.
- bookdown - R package to facilitate writing books and long-form articles, reports with R Markdown :bookmark: :link:.
- 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.
- Zettlr - Markdown editor which
integrates CSL, BibLaTeX, Pandoc and many other tools
:bookmark: :link:.
Bibliography
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.
- ZoteroBib - Online bibliography reference manager.
Illustrations
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.
Converters and Filters
Supplementary files and tools.
- Cicero - Python package which renders HTML presentations
from Markdown source using remark or reveal.js :link:.
- docutils - Python package which can
convert reStructuredText into various formats and provides command-line
tools to do it :link:.
- 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 :bookmark: :link:.
- 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 :bookmark: :link:.
Spell Checking and Linting
- 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.
Templates
Reusable minimalist examples.
Articles
Books
Tutorials
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 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.
- 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.
- 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.
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Contribute
Contributions welcome! Read the contribution guidelines first.