writing-resources/awesome-scientific-writing

Miscellaneous 2 months ago 444

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

Jul 31st

Converters and Filters

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

Tutorials

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.

May 26th

Word Processors

Marktext stars36.2k - Markdown text editor.

Converters and Filters

Jupyter Book - A static site generator which converts a collection of CommonMark, MyST markdown and Jupyter notebooks into a HTML website.

Mar 21st

Tutorials

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

Aug 25th, 2021

Other Lists

Awesome Jupyter stars2.9k

Awesome LaTeX stars1.1k

Awesome Markdown stars604

Delightful Open Science

Nov 29th, 2020

Converters and Filters

MyST - Markedly Structured Text, a superset of CommonMark markdown with reStructuredText like features.

May 24th, 2020

Templates

Articles

Pandoc Markdown-LaTeX Boilerplate stars93 - Demonstrate how to integrate Pandoc with an existing LaTeX template which requires some boilerplate code (i.e. LaTeX preamble), thus avoiding the latexmk dependency.

Apr 29th, 2020

Bibliography

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

ZoteroBib - Online bibliography reference manager.

Converters and Filters

pandoc - Haskell library for converting from one markup format to another, and a command-line tool that uses this library 🔖 🔗.

Academic Markdown stars334 - 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.

Templates

Books

Eisvogel stars4.5k - Clean academic pandoc LaTeX template.

Tutorials

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

Apr 8th, 2020

Spell Checking and Linting

GNU Aspell - Command line spell checker.

Hunspell - Command line spell checker.

Apr 7th, 2020

Word Processors

Atom - Popular IDE with Markdown support.

Markdown Preview Enhanced for Atom stars3.7k - Pandoc integration and utilities for Atom.
Autocomplete BibTeX for Atom stars44 - BibTeX support for Atom.

R Studio stars4.1k - IDE for R.

bookdown stars3.1k - R package to facilitate writing books and long-form articles, reports with R Markdown 🔖 🔗.
R Markdown - R package to write R next to Markdown

🔖 🔗.

Vim - Command line text editor.

fzf-bibtex stars90 - BibTeX source with Vim integration which uses fzf (a fuzzy finder implemented in Go).
vim-pandoc stars872 - Pandoc integration and utilities for Vim.
vim-pandoc-syntax stars386 - Pandoc syntax highlighting for Vim.

Visual Studio Code - Popular IDE with Markdown support.

Markdown All in One stars2.4k - Extension for enhanced Markdown support in VSCode, such as preview and auto completion to name a few.

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

Bibliography

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.

Illustrations

diagrams.net - Open source, online, desktop and container deployable diagramming software.

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.

Templates

Articles

Steve's R Markdown Templates stars813 - Academic manuscript, memos, Beamer presentation, syllabus and CV.

scientific-markdown stars39 - Example for use of Markdown for scientific publications using Pandoc and latexmk.

Tutorials

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

Book on Riemann solvers stars197 - 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.

Katrin Leinweber's Ph.D. thesis stars37 - Automated work flow involving several tools, but primarily Pandoc, latexmk and Academic Markdown.

Teaching and learning with Jupyter stars382 - 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.

Templates

Presentations

pandoc-starter stars487 - Templates for articles, Beamer presentations etc. using Markdown files and Makefiles for getting started with Pandoc.

slides stars2 - Demo for generating reveal.js presentations using Pandoc.

Templates

Books

bookdown-demo stars432 - Minimal example of a book based on R Markdown and bookdown.

Template for writing a PhD thesis in Markdown stars1.1k - 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.

Mar 21st, 2020

Converters and Filters

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

Mar 20th, 2020

Converters and Filters

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

Oct 7th, 2019

Converters and Filters

nbconvert - Convert Jupyter notebooks into reveal.js presentations, PDF, HTML, Markdown, reStructuredText and more.

Spell Checking and Linting

LanguageTool - Open source grammar, style and

Last Checked At: 2022-09-30T16:25:52.109Z

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Top 50 Awesome List

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Platforms

Programming Languages

Front-End Development

Back-End Development

Computer Science

Big Data

Theory

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Editors

Gaming

Development Environment

Entertainment

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Media

Learn

Security

Content Management Systems

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Business

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Decentralized Systems

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Miscellaneous

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writing-resources/awesome-scientific-writing

Converters and Filters

Tutorials

May 26th

Word Processors

Converters and Filters

Mar 21st

Tutorials

Aug 25th, 2021

Other Lists

Nov 29th, 2020

Converters and Filters

May 24th, 2020

Templates

Articles

Apr 29th, 2020

Bibliography

Converters and Filters

Templates

Books