awesome-awesomeness/terminal/scientificwriting2

                                                 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.