awesome-scientific-writing

Writing toolkit

A curated collection of tools and resources for scientific writing beyond LaTeX

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

GitHub

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last commit: over 2 years ago
Linked from 5 awesome lists

awesomeawesome-listjupyter-notebookmarkdownorg-modepandocrestructuredtext

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writing-resources.github.io/awesome-scientific-writing/

Awesome Scientific Writing / Word Processors

Marktext47,909about 2 years agoMarkdown text editor
R Studio4,716almost 2 years agoIDE for R

Awesome Scientific Writing / Word Processors / R Studio

bookdown3,811almost 2 years agoR package to facilitate writing books and long-form articles, reports with R Markdown
R MarkdownR package to write R next to Markdown

Awesome Scientific Writing / Word Processors

VimCommand line text editor

Awesome Scientific Writing / Word Processors / Vim

fzf-bibtex130about 2 years agoBibTeX source with Vim integration which uses fzf (a fuzzy finder implemented in Go)
vim-pandoc957about 2 years agoPandoc integration and utilities for Vim
vim-pandoc-syntax424over 2 years agoPandoc syntax highlighting for Vim

Awesome Scientific Writing / Word Processors

Visual Studio CodePopular IDE with Markdown support

Awesome Scientific Writing / Word Processors / Visual Studio Code

Markdown All in One2,942over 2 years agoExtension for enhanced Markdown support in VSCode, such as preview and auto completion to name a few
Markdown Preview Enhanced4,150about 2 years agoPandoc integration and utilities

Awesome Scientific Writing / Word Processors

ZettlrMarkdown editor which integrates CSL, BibLaTeX, Pandoc and many other tools

Awesome Scientific Writing / Bibliography

Citation Style Language (CSL) stylesCrowdsourced repository with over 9000 free CSL citation styles and an online editor to create new ones
JabRefOpen source bibliography reference manager
ZoteroFOSS tool to collect, organize, cite, and share research

Awesome Scientific Writing / Bibliography / Zotero

Better BibTeX for ZoteroEnhanced BibTeX / BibLaTeX integration for Zotero
ZotFile for ZoteroEnhanced PDF file management for Zotero

Awesome Scientific Writing / Bibliography

ZoteroBibOnline bibliography reference manager

Awesome Scientific Writing / Illustrations

app.diagrams.netOpen source, online, desktop and container deployable diagramming software named draw.io
graphvizVisualization software for graphs and networks which uses a domain-specific DOT language
Mermaid Live EditorDefine simple diagrams instead of drawing them
Vega LiteDefine charts and more complex diagrams
PlantUMLDefine UML diagrams instead of drawing them

Awesome Scientific Writing / Converters and Filters

CiceroPython package which renders HTML presentations from Markdown source using remark or reveal.js
docutilsPython package which can convert reStructuredText into various formats and provides command-line tools to do it
Jupyter BookA static site generator which converts a collection of CommonMark, MyST markdown and Jupyter notebooks into a HTML website
MySTMarkedly Structured Text, a superset of CommonMark markdown with reStructuredText like features
nbconvertConvert Jupyter notebooks into presentations, PDF, HTML, Markdown, reStructuredText and more
pandocHaskell library for converting from one markup format to another, and a command-line tool that uses this library

Awesome Scientific Writing / Converters and Filters / pandoc

Academic Markdown350over 5 years agoPython wrapper over Pandoc with specialized extensions to parse certain elements, making it a superset of Pandoc Markdown flavour
Pandoc filters35,082almost 2 years agoList of addons to pandoc which implement extra features such as citations and cross-references
PanflutePythonic alternative to John MacFarlane's pandocfilters

Awesome Scientific Writing / Converters and Filters

QuartoCompile R Markdown, and Jupyter Notebooks to PDFs, Slides and Websites. Supports R, Python, and Julia

Awesome Scientific Writing / Spell Checking and Linting

GNU AspellCommand line spell checker
HunspellCommand line spell checker
LanguageToolOpen source grammar, style and spell Checker
LanguageCheck98about 3 years agoAnalyses 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 tool1,831over 2 years agoMarkdown linter
proselint4,368about 2 years agoLinter for prose
remarklint949about 2 years agoMarkdown linter
restructuredtext-lint171over 4 years agoreStructuredText linter
textlintPluggable linting tool for text and Markdown
textidoteSpelling, grammar and style checking on LaTeX documents
Vale4,553almost 2 years agoFree, open-source linter for prose built with speed and extensibility in mind
write-good4,964almost 2 years agoNaive linter for English prose

Awesome Scientific Writing / Templates / Articles

Pandoc Markdown-LaTeX Boilerplate101over 8 years agoDemonstrate how to integrate Pandoc with an existing LaTeX template which requires some boilerplate code (i.e. LaTeX preamble), thus avoiding the dependency
scientific-markdown46over 11 years agoExample for use of Markdown for scientific publications using Pandoc and
Steve's R Markdown Templates908about 5 years agoAcademic manuscript, memos, Beamer presentation, syllabus and CV

Awesome Scientific Writing / Templates / Presentations

pandoc-starter533about 5 years agoTemplates for articles, Beamer presentations etc. using Markdown files and Makefiles for getting started with Pandoc
slides3over 9 years agoDemo for generating presentations using Pandoc

Awesome Scientific Writing / Templates / Books

bookdown-demo514almost 2 years agoMinimal example of a book based on R Markdown and bookdown
Eisvogel6,300almost 2 years agoClean academic pandoc LaTeX template
Template for writing a PhD thesis in Markdown1,214over 3 years agoClean 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

Awesome Scientific Writing / 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
Book on Riemann solvers267over 3 years agoThis example uses a custom template and shows how to store your notebooks with no output (for version control) while automatically executing them before running , so that PDF and HTML versions include the output
Dennis Tenen and Grant WythoffSustainable Authorship in Plain Text using Pandoc and Markdown
Heads up! Quarto is here to stay. Immediately combine R & Python in your next documentSummary 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. thesis45almost 5 years agoAutomated work flow involving several tools, but primarily Pandoc, and Academic Markdown
Scott SeliskerPlain Text Workflow for Academic Writing with Atom
Teaching and learning with Jupyter438over 3 years agoBook written in R Markdown, bookdown and also rendered as HTML, PDF and EPUB
Write your dissertation in RMarkdownStep-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-modeDetailed tutorial on authoring a paper by seamlessly integrating with LaTeX commands within Org-mode

Awesome Scientific Writing / Other Lists

Awesome Jupyter4,083almost 2 years ago
Awesome LaTeX1,419about 2 years ago
Awesome Markdown813about 2 years ago
Delightful Open Science

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