Marktext

Markdown text editor.

R Studio

IDE for R.

bookdown

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

R Markdown

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

Vim

Command line text editor.

fzf-bibtex

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

vim-pandoc

Pandoc integration and utilities for Vim.

vim-pandoc-syntax

Pandoc syntax highlighting for Vim.

Visual Studio Code

Popular IDE with Markdown support.

Markdown All in One

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

Markdown Preview Enhanced

Pandoc integration and utilities.

Zettlr

Markdown editor which integrates CSL, BibLaTeX, Pandoc and many other tools :bookmark: :link:.

Citation Style Language (CSL) styles

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

citecheck

Command-line tool that matches BibTeX, RIS, and CSL-JSON references against Crossref and OpenAlex and flags retractions reported by Crossref.

JabRef

Open source bibliography reference manager.

ScholarRef

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

Zotero

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

Better BibTeX for Zotero

Enhanced BibTeX / BibLaTeX integration for Zotero.

Zotero OCR

Plugin that makes scanned PDFs searchable using Tesseract OCR and Poppler.

ZoteroBib

Online bibliography reference manager.

app.diagrams.net

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

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.

Cicero

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

docutils

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

Jupyter Book

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

Manubot

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

latex2arxiv

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.

MyST

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

MyST Markdown CLI

Command-line tools for building scientific documents from MyST Markdown with citations, cross-references, and HTML, PDF, and Word output.

nbconvert

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

pandoc

Haskell library for converting from one markup format to another, and a command-line tool that uses this library :bookmark: :link:.

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.

Quarto

Compile R Markdown, and Jupyter Notebooks to PDFs, Slides and Websites. Supports R, Python, and Julia :bookmark: :link:.

Typst

Markup-based typesetting system with math, bibliography management, and fast incremental compilation to PDF.

GNU Aspell

Command line spell checker.

Hunspell

Command line spell checker.

LanguageTool

Open source grammar, style and spell Checker.

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

Markdown linter.

mdformat

Opinionated CommonMark-compliant Markdown formatter. Enforces consistent style (indentation, ATX headings, link references at bottom). Supports CommonMark by default, with plugins for GFM, tables, footnotes, admonitions, MyST, MkDocs, and more.

proselint

Linter for prose.

remarklint

Markdown linter.

restructuredtext-lint

reStructuredText linter.

rumdl

Fast Markdown linter and formatter written in Rust, with built-in support for several "flavors" such as GFM, MkDocs, MyST, Quarto etc.

textlint

Pluggable linting tool for text and Markdown.

textidote

Spelling, grammar and style checking on LaTeX documents.

Vale

Free, open-source linter for prose built with speed and extensibility in mind.

write-good

Naive linter for English prose.

Paper Templates for GitHub Pages

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

bookdown-demo

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

Eisvogel

Clean academic pandoc LaTeX template.

Template for writing a PhD thesis in Markdown

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.

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 solvers

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

Sustainable Authorship in Plain Text using Pandoc and Markdown.

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.

Write your dissertation in RMarkdown

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

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

Awesome Jupyter

Jupyter

Awesome LaTeX

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Awesome Markdown

Delightful Open Science