awesome-scientific-writing

Marktext

Markdown text editor

R Studio

IDE for R

bookdown

R package to facilitate writing books and long-form articles, reports with R Markdown

R package to write R next to Markdown

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

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

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

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

Open source bibliography reference manager

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

Enhanced BibTeX / BibLaTeX integration for Zotero

Enhanced PDF file management for Zotero

Online bibliography reference manager

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 charts and more complex diagrams

Define UML diagrams instead of drawing them

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

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

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

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

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

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

Academic Markdown

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

Pythonic alternative to John MacFarlane's pandocfilters

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

Command line spell checker

Command line spell checker

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

proselint

Linter for prose

remarklint

Markdown linter

restructuredtext-lint

reStructuredText linter

Pluggable linting tool for text and Markdown

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

Pandoc Markdown-LaTeX Boilerplate

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

scientific-markdown

Example for use of Markdown for scientific publications using Pandoc and

Steve's R Markdown Templates

Academic manuscript, memos, Beamer presentation, syllabus and CV

pandoc-starter

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

slides

Demo for generating presentations using Pandoc

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

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 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

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

Katrin Leinweber's Ph.D. thesis

Automated work flow involving several tools, but primarily Pandoc, and Academic Markdown

Plain Text Workflow for Academic Writing with Atom

Teaching and learning with Jupyter

Book written in R Markdown, bookdown and also rendered as HTML, PDF and EPUB

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