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https://github.com/writing-resources/awesome-scientific-writing

:keyboard: A curated list of awesome tools, demos and resources to go beyond LaTeX
https://github.com/writing-resources/awesome-scientific-writing

List: awesome-scientific-writing

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:keyboard: A curated list of awesome tools, demos and resources to go beyond LaTeX

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# Awesome Scientific Writing [![Awesome](https://awesome.re/badge-flat.svg)](https://github.com/sindresorhus/awesome)



> Scientific writing can extend beyond LaTeX, made possible by formats,

> such as

> [Markdown](https://daringfireball.net/projects/markdown/) (and its many flavours),

> [reStructuredText](https://docutils.sourceforge.io/rst.html) and

> [Jupyter notebooks](https://jupyter.org/).



:bookmark: means ability to **seamlessly cite references**.



:link: means ability to **cross-reference figures and sections within the

document**.



## Contents



- [Word Processors](#word-processors)

- [Bibliography](#bibliography)

- [Illustrations](#illustrations)

- [Converters and Filters](#converters-and-filters)

- [Spell Checking and Linting](#spell-checking-and-linting)

- [Templates](#templates)

  - [Articles](#articles)

  - [Presentations](#presentations)

  - [Books](#books)

- [Tutorials](#tutorials)

- [Other Lists](#other-lists)



## Word Processors



- [Marktext](https://marktext.app/) - Markdown text editor.

- [R Studio](https://github.com/rstudio/rstudio) - IDE for R.

  - [bookdown](https://github.com/rstudio/bookdown) - R package to facilitate writing books and long-form articles, reports with R Markdown :bookmark: :link:.

  - [R Markdown](https://rmarkdown.rstudio.com/) - R package to write R next to Markdown

   :bookmark:

   :link:.

- [Vim](https://www.vim.org/) - Command line text editor.

  - [fzf-bibtex](https://github.com/msprev/fzf-bibtex/#readme) - BibTeX source

    with Vim integration which uses fzf (a fuzzy finder implemented in Go).

  - [vim-pandoc](https://github.com/vim-pandoc/vim-pandoc) - Pandoc integration and utilities for Vim.

  - [vim-pandoc-syntax](https://github.com/vim-pandoc/vim-pandoc-syntax) - Pandoc syntax highlighting for Vim.

- [Visual Studio Code](https://code.visualstudio.com/) - Popular IDE with Markdown support.

  - [Markdown All in One](https://github.com/yzhang-gh/vscode-markdown/#readme) - Extension for enhanced

    Markdown support in VSCode, such as preview and auto completion to name a few.

  - [Markdown Preview Enhanced](https://github.com/shd101wyy/markdown-preview-enhanced) - Pandoc

    integration and utilities.  

- [Zettlr](https://www.zettlr.com/) - 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](https://editor.citationstyles.org/) - Crowdsourced

  repository with over 9000 free CSL citation styles and an online

  editor to create new ones.

- [JabRef](https://www.jabref.org/) - Open source bibliography reference manager.

- [Zotero](https://www.zotero.org/) - FOSS tool to collect, organize, cite, and

  share research.

  - [Better BibTeX for Zotero](https://retorque.re/zotero-better-bibtex/) - Enhanced

    BibTeX / BibLaTeX integration for Zotero.

  - [ZotFile for Zotero](http://zotfile.com/) - Enhanced PDF file management for Zotero.

- [ZoteroBib](https://zbib.org/) - 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](https://app.diagrams.net/) - Open source, online, desktop and

  container deployable diagramming software named draw.io.

- [graphviz](https://graphviz.org/) - Visualization software for graphs and

  networks which uses a domain-specific DOT language.

- [Mermaid Live Editor](https://mermaid-js.github.io/mermaid-live-editor/) - Define simple diagrams instead of drawing them.

- [Vega Lite](https://vega.github.io/vega-lite/examples/) - Define charts and more complex diagrams.

- [PlantUML](https://plantuml.com/) - Define UML diagrams instead of drawing them.



## Converters and Filters



Supplementary files and tools.



- [Cicero](https://cicero.xyz/) - Python package which renders HTML presentations

  from Markdown source using remark or reveal.js :link:.

- [docutils](https://docutils.sourceforge.io/docs/) - Python package which can

  convert reStructuredText into various formats and provides command-line

  tools to do it :link:.

- [Jupyter Book](https://jupyterbook.org/en/stable/) - A static site generator which converts

  a collection of CommonMark, MyST markdown and Jupyter notebooks into a HTML website.

- [MyST](https://myst-parser.readthedocs.io/en/latest/) - Markedly Structured Text,

  a superset of CommonMark markdown with reStructuredText like features.

- [nbconvert](https://nbconvert.readthedocs.io/en/latest/) - Convert Jupyter

  notebooks into `reveal.js` presentations, PDF, HTML, Markdown,

  reStructuredText and more.

- [pandoc](https://pandoc.org/MANUAL) - Haskell library for converting from

  one markup format to another, and a command-line tool that uses this

  library :bookmark: :link:.

  - [Academic Markdown](https://github.com/smathot/academicmarkdown#readme) - Python wrapper over Pandoc with specialized extensions to parse certain

    elements, making it a superset of Pandoc Markdown flavour :bookmark:

    :link:.

  - [Pandoc filters](https://github.com/jgm/pandoc/wiki/Pandoc-Filters) - List of

    addons to pandoc which implement extra features such as citations and

    cross-references.

  - [Panflute](http://scorreia.com/software/panflute/) - Pythonic alternative

    to John MacFarlane's pandocfilters.

- [Quarto](https://quarto.org) - Compile R Markdown, and Jupyter Notebooks to PDFs, Slides and Websites. Supports R, Python, and Julia :bookmark: :link:.



## Spell Checking and Linting



- [GNU Aspell](http://aspell.net/) - Command line spell checker.

- [Hunspell](http://hunspell.github.io/) - Command line spell checker.

- [LanguageTool](https://languagetool.org/) - Open source grammar, style and

 spell Checker.

- [LanguageCheck](https://github.com/JohannesBuchner/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](https://github.com/markdownlint/markdownlint) - Markdown linter.

- [proselint](https://github.com/amperser/proselint) - Linter for prose.

- [remarklint](https://github.com/remarkjs/remark-lint) - Markdown linter.

- [restructuredtext-lint](https://github.com/twolfson/restructuredtext-lint) - reStructuredText linter.

- [textlint](https://textlint.github.io/) - Pluggable linting tool for text

 and Markdown.

- [textidote](https://sylvainhalle.github.io/textidote/) - Spelling, grammar and

 style checking on LaTeX documents.

- [Vale](https://github.com/errata-ai/vale) - Free, open-source linter for

 prose built with speed and extensibility in mind.

- [write-good](https://github.com/btford/write-good) - Naive linter for English

 prose.



## Templates



Reusable minimalist examples.



### Articles



- [Pandoc Markdown-LaTeX

   Boilerplate](https://github.com/davecap/markdown-latex-boilerplate/#readme) - 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](https://github.com/JensErat/scientific-markdown/#readme) - Example

   for use of Markdown for scientific publications using Pandoc and

   `latexmk`.

- [Steve's R Markdown Templates](https://github.com/svmiller/svm-r-markdown-templates/) - Academic manuscript, memos, Beamer presentation, syllabus and CV.



### Presentations



- [pandoc-starter](https://github.com/jez/pandoc-starter/#readme) - Templates for

   articles, Beamer presentations etc. using Markdown files and Makefiles for

   getting started with Pandoc.

- [slides](https://github.com/cgroll/slides/#readme) - Demo for generating `reveal.js`

   presentations using Pandoc.



### Books



- [bookdown-demo](https://github.com/rstudio/bookdown-demo/#readme) - Minimal

   example of a book based on R Markdown and bookdown.

- [Eisvogel](https://github.com/Wandmalfarbe/pandoc-latex-template) - Clean academic pandoc LaTeX template.

- [Template for writing a PhD thesis in

   Markdown](https://github.com/tompollard/phd_thesis_markdown#readme) - 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



How to generate articles and presentations for scientific purposes.



- [3 frameworks into one — Write your next paper with R Studio!](https://blog.devgenius.io/write-your-whole-paper-in-r-it-is-better-77e1843f0c09) - 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](https://github.com/clawpack/riemann_book/#readme) - 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](https://programminghistorian.org/en/lessons/sustainable-authorship-in-plain-text-using-pandoc-and-markdown) - Sustainable Authorship in Plain Text using Pandoc and Markdown.

- [Heads up! Quarto is here to stay. Immediately combine R & Python in your next document](https://blog.devgenius.io/heads-up-quarto-is-here-to-stay-aa861ef87491) - 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](https://github.com/katrinleinweber/PhD-thesis/#readme) - Automated

   work flow involving several tools, but primarily Pandoc, `latexmk` and

   Academic Markdown.

- [Scott Selisker](https://u.arizona.edu/~selisker/post/workflow/) - Plain Text Workflow for Academic Writing with Atom.

- [Teaching and learning with

   Jupyter](https://github.com/jupyter4edu/jupyter-edu-book/#readme) - Book

   written in R Markdown, bookdown and also rendered as HTML, PDF and

   EPUB.

- [Write your dissertation in RMarkdown](https://ourcodingclub.github.io/tutorials/rmarkdown-dissertation/) - 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](https://www.draketo.de/english/emacs/writing-papers-in-org-mode-acpd) - Detailed

   tutorial on authoring a paper by seamlessly integrating with LaTeX

   commands within Org-mode.



## Other Lists



- [Awesome Jupyter](https://github.com/markusschanta/awesome-jupyter/#renderingpublishingconversion)

- [Awesome LaTeX](https://github.com/egeerardyn/awesome-LaTeX/#readme)

- [Awesome Markdown](https://github.com/BubuAnabelas/awesome-markdown/#readme)

- [Delightful Open Science](https://codeberg.org/teaserbot-labs/delightful-open-science)



### Contribute



Contributions welcome! Read the [contribution guidelines](CONTRIBUTING.md) first.