awesome-scientific-writing

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.

This example uses a custom

Sustainable Authorship in Plain Text using Pandoc and Markdown.

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.

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

Detailed tutorial on authoring a paper by seamlessly integrating with LaTeX commands within Org-mode.

Open source, online, desktop and container deployable diagramming software named draw.io.

Visualization software for graphs and networks which uses a domain-specific DOT language.

Define simple diagrams instead of drawing them.

Define UML diagrams instead of drawing them.

Define charts and more complex diagrams.

Enhanced BibTeX / BibLaTeX integration for Zotero.

Crowdsourced repository with over 9000 free CSL citation styles and an online editor to create new ones.

Open source bibliography reference manager.

Convert citation styles (APA 7, Harvard, Vancouver) directly inside Word

FOSS tool to collect, organize, cite, and share research.

Online bibliography reference manager.

R package to facilitate writing books and long-form articles, reports with R Markdown :bookmark: :link:.

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

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

Pandoc integration and utilities.

Markdown text editor.

R package to write R next to Markdown :bookmark: :link:.

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

Clean academic pandoc LaTeX template.

Markdown-based templates for papers and RESUME/CVs, publishing with GitHub Pages.

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.

Python package which renders HTML presentations from Markdown source using remark or reveal.js :link:.

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

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

Command-line tool which converts a LaTeX project into an arXiv-ready ZIP: prunes unused files, strips comments and draft markup, and flags arXiv submission blockers before upload.

Workflow for writing and publishing scholarly manuscripts with Markdown, persistent-identifier citations, and reproducible builds.

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

Command line spell checker.

Command line spell checker.

Analyses scientific LaTeX papers, suggesting improvements from a list of common mistakes/ambiguities, tense consistency, a vs. an, spell check, and paragraph topic sentences.

Open source grammar, style and spell Checker.

Markdown linter.

Linter for prose.