Research Tools
Software for reference management, finding literature, PDFs, transcription, Markdown writing, diagrams, open science, and data science.
Reference management
- Add-ons
- Better BibTex
- Zutilo
- ZotMoov — Plugin that moves Zotero attachments to a folder you choose and keeps them linked.
- scite Zotero plugin — Shows how often your saved papers are cited as supporting, contrasting, or mentioning.
- doi2bib — Paste a DOI and get a BibTeX entry back.
- AnyStyle — Parses a pasted reference list, in any citation style, into structured bibliographic data.
- Crossref Simple Text Query — Paste a reference list or bibliography to look up DOIs for each entry.
- JabRef — Open-source desktop reference manager with native support for BibTeX and BibLaTeX.
Finding literature
- Unpaywall — Finds legal open-access copies of paywalled articles.
- ResearchRabbit — Starts from one paper and maps related and citing work; it is AI-assisted, so check its suggestions against the papers themselves.
- Dimensions — Research database linking publications, grants, datasets, patents, and policy documents.
- Consensus — AI search engine over peer-reviewed literature; always read the cited papers before relying on its answers.
PDFs
- Sioyek — Free PDF viewer built for reading textbooks and research papers.
- Skim — Lightweight PDF reader and note-taker for macOS, designed for reading and annotating academic papers.
- OCRmyPDF — Adds a searchable text layer to scanned PDFs.
- Stirling-PDF — Open-source app for editing, merging, splitting, and converting PDFs; can run on your own machine.
- Mathpix — Converts images and PDFs, including equations, to LaTeX, Markdown, Word, and other formats.
Transcription
- Whisper — OpenAI’s open-source speech recognition model, which can run locally for interview transcripts.
- oTranscribe — Free browser tool for transcribing recorded interviews by hand, with playback controls beside the text.
- Vibe — Desktop app for transcribing audio on your own computer.
Note taking
- Zettlr
- Obsidian
- Obsidian Zotero Integration — Community plugin for inserting citations, literature notes, and annotations from Zotero into Obsidian.
- Raindrop.io — Bookmark manager.
Writing & Markdown
- Pandoc demos — Worked examples of converting between Markdown, LaTeX, Word, HTML, and other formats with Pandoc.
- Eisvogel pandoc LaTeX template — Template for turning Markdown into clean PDF or LaTeX with Pandoc.
- Markdown Guide: Extended Syntax — Reference for tables, footnotes, and other features beyond basic Markdown.
- Tables Generator — Builds LaTeX, Markdown, or HTML tables from pasted spreadsheet data.
- Links and Hypertext — WebAIM’s guidance on writing clear, descriptive link text for web pages and online documents.
Diagrams
- draw.io (diagrams.net) — Free diagramming app for flowcharts and concept maps.
- Mermaid — Draws flowcharts and other diagrams from Markdown-like text.
Open science
- OSF — Open Science Framework for sharing project files, data, and preregistrations.
- Referencing and citing content — GitHub Docs: how to make a repository citable, for example with a DOI.
- Open Scientific Code using Git and GitHub — Workshop materials for researchers learning to contribute to open-source code.
- Software Carpentry: Version Control with Git — Beginner lessons on tracking your work with Git.
Ebooks
- calibre — Free e-book manager and converter.
Data science
- RStudio — Editor (IDE) for R.
- Jupyter — Notebooks that combine code, results, and text, mainly for Python.
- Positron — Posit’s editor for R and Python.
- Quarto — Publishing system for reports, websites, and slides built from code and Markdown.
- R — Programming language for statistics and data analysis.
- ollama — Runs large language models on your own computer; see the Ollama setup guide.
- Sublime Text — Text and code editor.
- VS Code — Code editor from Microsoft.