292 lines
13 KiB
HTML
292 lines
13 KiB
HTML
<h1 id="awesome-scientific-writing-awesome">Awesome Scientific Writing
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<a href="https://github.com/sindresorhus/awesome"><img
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src="https://awesome.re/badge-flat.svg" alt="Awesome" /></a></h1>
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<blockquote>
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<p>Scientific writing can extend beyond LaTeX, made possible by formats,
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such as <a
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href="https://daringfireball.net/projects/markdown/">Markdown</a> (and
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its many flavours), <a
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href="https://docutils.sourceforge.io/rst.html">reStructuredText</a> and
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<a href="https://jupyter.org/">Jupyter notebooks</a>.</p>
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</blockquote>
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<p>:bookmark: means ability to <strong>seamlessly cite
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references</strong>.</p>
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<p>:link: means ability to <strong>cross-reference figures and sections
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within the document</strong>.</p>
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<h2 id="contents">Contents</h2>
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<ul>
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<li><a href="#word-processors">Word Processors</a></li>
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<li><a href="#bibliography">Bibliography</a></li>
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<li><a href="#illustrations">Illustrations</a></li>
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<li><a href="#converters-and-filters">Converters and Filters</a></li>
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<li><a href="#spell-checking-and-linting">Spell Checking and
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Linting</a></li>
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<li><a href="#templates">Templates</a>
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<ul>
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<li><a href="#articles">Articles</a></li>
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<li><a href="#presentations">Presentations</a></li>
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<li><a href="#books">Books</a></li>
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</ul></li>
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<li><a href="#tutorials">Tutorials</a></li>
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<li><a href="#other-lists">Other Lists</a></li>
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</ul>
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<h2 id="word-processors">Word Processors</h2>
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<ul>
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<li><a href="https://github.com/marktext/marktext">Marktext</a> -
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Markdown text editor.</li>
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<li><a href="https://github.com/rstudio/rstudio">R Studio</a> - IDE for
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R.
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<ul>
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<li><a href="https://github.com/rstudio/bookdown">bookdown</a> - R
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package to facilitate writing books and long-form articles, reports with
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R Markdown :bookmark: :link:.</li>
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<li><a href="https://rmarkdown.rstudio.com/">R Markdown</a> - R package
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to write R next to Markdown :bookmark: :link:.</li>
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</ul></li>
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<li><a href="https://www.vim.org/">Vim</a> - Command line text editor.
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<ul>
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<li><a
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href="https://github.com/msprev/fzf-bibtex/#readme">fzf-bibtex</a> -
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BibTeX source with Vim integration which uses fzf (a fuzzy finder
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implemented in Go).</li>
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<li><a href="https://github.com/vim-pandoc/vim-pandoc">vim-pandoc</a> -
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Pandoc integration and utilities for Vim.</li>
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<li><a
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href="https://github.com/vim-pandoc/vim-pandoc-syntax">vim-pandoc-syntax</a>
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- Pandoc syntax highlighting for Vim.</li>
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</ul></li>
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<li><a href="https://code.visualstudio.com/">Visual Studio Code</a> -
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Popular IDE with Markdown support.
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<ul>
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<li><a
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href="https://github.com/yzhang-gh/vscode-markdown/#readme">Markdown All
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in One</a> - Extension for enhanced Markdown support in VSCode, such as
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preview and auto completion to name a few.</li>
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<li><a
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href="https://github.com/shd101wyy/markdown-preview-enhanced">Markdown
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Preview Enhanced</a> - Pandoc integration and utilities.<br />
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</li>
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</ul></li>
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<li><a href="https://www.zettlr.com/">Zettlr</a> - Markdown editor which
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integrates CSL, BibLaTeX, Pandoc and many other tools :bookmark:
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:link:.</li>
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</ul>
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<h2 id="bibliography">Bibliography</h2>
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<p>Reference managers to generate citations, BibTeX, and BibLaTeX
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files.</p>
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<ul>
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<li><a href="https://editor.citationstyles.org/">Citation Style Language
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(CSL) styles</a> - Crowdsourced repository with over 9000 free CSL
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citation styles and an online editor to create new ones.</li>
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<li><a href="https://www.jabref.org/">JabRef</a> - Open source
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bibliography reference manager.</li>
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<li><a href="https://www.zotero.org/">Zotero</a> - FOSS tool to collect,
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organize, cite, and share research.
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<ul>
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<li><a href="https://retorque.re/zotero-better-bibtex/">Better BibTeX
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for Zotero</a> - Enhanced BibTeX / BibLaTeX integration for Zotero.</li>
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<li><a href="http://zotfile.com/">ZotFile for Zotero</a> - Enhanced PDF
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file management for Zotero.</li>
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</ul></li>
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<li><a href="https://zbib.org/">ZoteroBib</a> - Online bibliography
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reference manager.</li>
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</ul>
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<h2 id="illustrations">Illustrations</h2>
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<p>Drawing illustrations themselves has driven many a scientist mad.
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Fortunately, there are formal languages with which one can create
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beautiful graphics.</p>
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<ul>
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<li><a href="https://app.diagrams.net/">app.diagrams.net</a> - Open
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source, online, desktop and container deployable diagramming software
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named draw.io.</li>
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<li><a href="https://graphviz.org/">graphviz</a> - Visualization
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software for graphs and networks which uses a domain-specific DOT
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language.</li>
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<li><a href="https://mermaid-js.github.io/mermaid-live-editor/">Mermaid
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Live Editor</a> - Define simple diagrams instead of drawing them.</li>
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<li><a href="https://vega.github.io/vega-lite/examples/">Vega Lite</a> -
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Define charts and more complex diagrams.</li>
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<li><a href="https://plantuml.com/">PlantUML</a> - Define UML diagrams
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instead of drawing them.</li>
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</ul>
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<h2 id="converters-and-filters">Converters and Filters</h2>
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<p>Supplementary files and tools.</p>
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<ul>
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<li><a href="https://cicero.xyz/">Cicero</a> - Python package which
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renders HTML presentations from Markdown source using remark or
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reveal.js :link:.</li>
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<li><a href="https://docutils.sourceforge.io/docs/">docutils</a> -
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Python package which can convert reStructuredText into various formats
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and provides command-line tools to do it :link:.</li>
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<li><a href="https://jupyterbook.org/en/stable/">Jupyter Book</a> - A
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static site generator which converts a collection of CommonMark, MyST
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markdown and Jupyter notebooks into a HTML website.</li>
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<li><a href="https://myst-parser.readthedocs.io/en/latest/">MyST</a> -
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Markedly Structured Text, a superset of CommonMark markdown with
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reStructuredText like features.</li>
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<li><a href="https://nbconvert.readthedocs.io/en/latest/">nbconvert</a>
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- Convert Jupyter notebooks into <code>reveal.js</code> presentations,
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PDF, HTML, Markdown, reStructuredText and more.</li>
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<li><a href="https://pandoc.org/MANUAL">pandoc</a> - Haskell library for
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converting from one markup format to another, and a command-line tool
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that uses this library :bookmark: :link:.
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<ul>
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<li><a
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href="https://github.com/smathot/academicmarkdown#readme">Academic
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Markdown</a> - Python wrapper over Pandoc with specialized extensions to
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parse certain elements, making it a superset of Pandoc Markdown flavour
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:bookmark: :link:.</li>
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<li><a href="https://github.com/jgm/pandoc/wiki/Pandoc-Filters">Pandoc
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filters</a> - List of addons to pandoc which implement extra features
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such as citations and cross-references.</li>
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<li><a href="http://scorreia.com/software/panflute/">Panflute</a> -
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Pythonic alternative to John MacFarlane’s pandocfilters.</li>
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</ul></li>
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<li><a href="https://quarto.org">Quarto</a> - Compile R Markdown, and
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Jupyter Notebooks to PDFs, Slides and Websites. Supports R, Python, and
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Julia :bookmark: :link:.</li>
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</ul>
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<h2 id="spell-checking-and-linting">Spell Checking and Linting</h2>
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<ul>
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<li><a href="http://aspell.net/">GNU Aspell</a> - Command line spell
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checker.</li>
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<li><a href="http://hunspell.github.io/">Hunspell</a> - Command line
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spell checker.</li>
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<li><a href="https://languagetool.org/">LanguageTool</a> - Open source
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grammar, style and spell Checker.</li>
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<li><a
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href="https://github.com/JohannesBuchner/languagecheck">LanguageCheck</a>
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- Analyses scientific LaTeX papers, suggesting improvements from a list
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of common mistakes/ambiguities, tense consistency, a vs. an, spell
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check, and paragraph topic sentences.</li>
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<li><a href="https://github.com/markdownlint/markdownlint">Markdown lint
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tool</a> - Markdown linter.</li>
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<li><a href="https://github.com/amperser/proselint">proselint</a> -
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Linter for prose.</li>
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<li><a href="https://github.com/remarkjs/remark-lint">remarklint</a> -
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Markdown linter.</li>
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<li><a
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href="https://github.com/twolfson/restructuredtext-lint">restructuredtext-lint</a>
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- reStructuredText linter.</li>
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<li><a href="https://textlint.github.io/">textlint</a> - Pluggable
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linting tool for text and Markdown.</li>
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<li><a href="https://sylvainhalle.github.io/textidote/">textidote</a> -
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Spelling, grammar and style checking on LaTeX documents.</li>
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<li><a href="https://github.com/errata-ai/vale">Vale</a> - Free,
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open-source linter for prose built with speed and extensibility in
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mind.</li>
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<li><a href="https://github.com/btford/write-good">write-good</a> -
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Naive linter for English prose.</li>
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</ul>
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<h2 id="templates">Templates</h2>
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<p>Reusable minimalist examples.</p>
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<h3 id="articles">Articles</h3>
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<ul>
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<li><a
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href="https://github.com/davecap/markdown-latex-boilerplate/#readme">Pandoc
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Markdown-LaTeX Boilerplate</a> - Demonstrate how to integrate Pandoc
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with an existing LaTeX template which requires some boilerplate code
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(i.e. LaTeX preamble), thus avoiding the <code>latexmk</code>
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dependency.</li>
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<li><a
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href="https://github.com/JensErat/scientific-markdown/#readme">scientific-markdown</a>
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- Example for use of Markdown for scientific publications using Pandoc
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and <code>latexmk</code>.</li>
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<li><a
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href="https://github.com/svmiller/svm-r-markdown-templates/">Steve’s R
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Markdown Templates</a> - Academic manuscript, memos, Beamer
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presentation, syllabus and CV.</li>
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</ul>
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<h3 id="presentations">Presentations</h3>
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<ul>
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<li><a
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href="https://github.com/jez/pandoc-starter/#readme">pandoc-starter</a>
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- Templates for articles, Beamer presentations etc. using Markdown files
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and Makefiles for getting started with Pandoc.</li>
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<li><a href="https://github.com/cgroll/slides/#readme">slides</a> - Demo
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for generating <code>reveal.js</code> presentations using Pandoc.</li>
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</ul>
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<h3 id="books">Books</h3>
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<ul>
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<li><a
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href="https://github.com/rstudio/bookdown-demo/#readme">bookdown-demo</a>
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- Minimal example of a book based on R Markdown and bookdown.</li>
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<li><a
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href="https://github.com/Wandmalfarbe/pandoc-latex-template">Eisvogel</a>
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- Clean academic pandoc LaTeX template.</li>
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<li><a
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href="https://github.com/tompollard/phd_thesis_markdown#readme">Template
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for writing a PhD thesis in Markdown</a> - Clean organization of files
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to provide a framework for writing a PhD thesis in mostly Markdown with
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a little bit of LaTeX, and compiled with Pandoc.</li>
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</ul>
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<h2 id="tutorials">Tutorials</h2>
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<p>How to generate articles and presentations for scientific
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purposes.</p>
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<ul>
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<li><a
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href="https://blog.devgenius.io/write-your-whole-paper-in-r-it-is-better-77e1843f0c09">3
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frameworks into one — Write your next paper with R Studio!</a> - Article
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provides an overview to a workflow that combines R Markdown (bookdown),
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Zotero (literature management), and Notion (note taking on research
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papers) to write academic papers.</li>
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<li><a href="https://github.com/clawpack/riemann_book/#readme">Book on
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Riemann solvers</a> - This example uses a custom <code>nbconvert</code>
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template and shows how to store your notebooks with no output (for
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version control) while automatically executing them before running
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<code>bookbook</code>, so that PDF and HTML versions include the
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output.</li>
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<li><a
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href="https://programminghistorian.org/en/lessons/sustainable-authorship-in-plain-text-using-pandoc-and-markdown">Dennis
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Tenen and Grant Wythoff</a> - Sustainable Authorship in Plain Text using
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Pandoc and Markdown.</li>
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<li><a
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href="https://blog.devgenius.io/heads-up-quarto-is-here-to-stay-aa861ef87491">Heads
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up! Quarto is here to stay. Immediately combine R & Python in your
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next document</a> - Summary of the capabilities of Quarto, why to use
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it, and how it compares to R Markdown. Also contains tips for M1 Mac
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users on how to fix a common problem with reticulate.</li>
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<li><a
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href="https://github.com/katrinleinweber/PhD-thesis/#readme">Katrin
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Leinweber’s Ph.D. thesis</a> - Automated work flow involving several
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tools, but primarily Pandoc, <code>latexmk</code> and Academic
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Markdown.</li>
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<li><a href="https://u.arizona.edu/~selisker/post/workflow/">Scott
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Selisker</a> - Plain Text Workflow for Academic Writing with Atom.</li>
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<li><a
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href="https://github.com/jupyter4edu/jupyter-edu-book/#readme">Teaching
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and learning with Jupyter</a> - Book written in R Markdown, bookdown and
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also rendered as HTML, PDF and EPUB.</li>
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<li><a
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href="https://ourcodingclub.github.io/tutorials/rmarkdown-dissertation/">Write
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your dissertation in RMarkdown</a> - Step-by-step guide on creating a
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complex pdf document, including text, figures, references, images,
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formatting, and more.</li>
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<li><a
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href="https://www.draketo.de/english/emacs/writing-papers-in-org-mode-acpd">Writing
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scientific papers for ACPD using Emacs Org-mode</a> - Detailed tutorial
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on authoring a paper by seamlessly integrating with LaTeX commands
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within Org-mode.</li>
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</ul>
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<h2 id="other-lists">Other Lists</h2>
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<ul>
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<li><a
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href="https://github.com/markusschanta/awesome-jupyter/#renderingpublishingconversion">Awesome
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Jupyter</a></li>
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<li><a
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href="https://github.com/egeerardyn/awesome-LaTeX/#readme">Awesome
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LaTeX</a></li>
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<li><a
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href="https://github.com/BubuAnabelas/awesome-markdown/#readme">Awesome
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Markdown</a></li>
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<li><a
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href="https://codeberg.org/teaserbot-labs/delightful-open-science">Delightful
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Open Science</a></li>
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</ul>
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<h3 id="contribute">Contribute</h3>
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<p>Contributions welcome! Read the <a
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href="CONTRIBUTING.md">contribution guidelines</a> first.</p>
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<p><a
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href="https://github.com/writing-resources/awesome-scientific-writing">scientificwriting.md
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Github</a></p>
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