Recommendations
Recommended tools, services, R packages, Zotero plugins, books, and online learning resources.
Note
Original Japanese version: おすすめ
This page collects tools, services, books, and online resources that I use personally or want to keep as references. The list focuses on resources that are available online and useful for research, writing, programming, data analysis, and everyday knowledge work. I update it as my workflow changes.
Tools and Services
Notes and Literature Management
- Obsidian: A Markdown-based note-taking app with strong linking and tagging features.
- Zotero: A reference manager for collecting, organizing, citing, and annotating research literature.
- Elicit: An AI-assisted research tool for literature search, summaries, and evidence discovery.
- Google Scholar | Labs: Experimental search features from Google Scholar.
- Undermind: An AI search tool for exploring research literature.
- ResearchRabbit: A literature discovery tool that visualizes relationships among papers and helps find related work.
Development and Documentation
Information Collection and Task Management
- Raindrop.io: A bookmark manager.
- Karakeep: A self-hostable bookmark manager. I installed it as a possible alternative to Raindrop.io, although I have not fully integrated it into my workflow yet.
- VisiOS: A tool for managing bookmarks and browser tabs.
- Inoreader: An RSS reader.
- Todoist: A task-management app.
Images, Video, and Streaming
- Eagle: An image-management tool with tagging and collection features.
- Affinity: Image and photo editing software that can serve as an alternative to Adobe Photoshop and Illustrator.
- Kdenlive: Video-editing software.
- OBS Studio: Software for screen recording and live streaming.
- Keyviz: An open-source keyboard visualizer.
Security and Networking
- Bitwarden: A password manager.
- Proton Mail: A secure email service.
- Proton Authenticator: A two-factor authentication app.
- Tailscale: A VPN service based on WireGuard.
- NordVPN: A VPN service. I am considering switching to Proton VPN.
- RustDesk: Remote desktop software and an alternative to AnyDesk.
- Brave: A privacy-focused web browser.
- Element: An open-source chat app based on the Matrix protocol.
AI
- LM Studio: A local AI chat tool that is useful for trying local LLMs.
R Packages
- tmap: An R package specialized for creating maps and visualizing geospatial data.
- rnaturalearth: An R package that provides natural-earth data such as country borders and physical geography.
- cols4all: An R package for color palettes, including palettes designed with color-vision diversity in mind.
Zotero Plugins
- Better BibTeX for Zotero: Useful for connecting Zotero with external tools such as Obsidian.
- Ethereal Style: A plugin that extends the Zotero user interface.
- ZotCard: A plugin for card-style notes and note templates.
- Zotero Reading List: A plugin for managing literature reading status, such as unread, reading, and finished.
- ZotSeek: A plugin that helps search for similar literature.
- Zotero Better Notes: A plugin that enhances Zotero’s note-taking features.
- Zotodo: A plugin that connects Zotero with task-management apps such as Todoist.
- Zotero Reference: A plugin that helps with cited-reference access and reference-list workflows.
Books and Online Resources
Plants and Morphology
- Manual of Leaf Architecture: A manual on leaf morphology. It provides foundational knowledge for understanding leaf architecture. License: CC BY-NC 4.0.
- Contributions to Morphometrics: A classic resource on morphometrics.
R
These are high-quality R books and resources that can be read online.
- R for Data Science (2e): An introductory book on data science with R, covering data handling, visualization, modeling, and more. License: CC BY-NC-ND 3.0.
- R Graphics Cookbook, 2nd edition: A recipe-style book on R graphics, with many examples using ggplot2.
- Cookbook for R: A recipe collection for a wide range of R tasks. License: CC0.
- Tidy Modeling with R: An introductory book on modeling with tidymodels.
- Efficient R programming: A practical book on writing efficient R code.
- Big Book of R: A curated collection of online R learning resources.
- Mastering Shiny: An introductory book on Shiny by Hadley Wickham.
- Deep Learning with R: A book on deep learning with R.
- blogdown: Creating Websites with R Markdown: A book on building websites with blogdown.
- Mastering Spark with R: A book on using Spark from R.
- R Packages (2e): An introductory book on R package development.
- ggplot2: Elegant Graphics for Data Analysis (3e): An introductory book on ggplot2.
Python
- Think Python: An introductory book on Python.
- Think Python, 2nd edition: The second edition of Think Python.
- Cracking Codes with Python: A book for learning Python through cryptography examples.
- Beyond the Basic Stuff with Python: A book to read after learning Python basics.
- The Big Book of Small Python Projects: A book for learning through small Python projects.
- Python for Data Analysis, 3E: A standard book on data analysis with Python, especially pandas.
- Introduction to Statistics for Data Analysis: Introductory material on statistics for data analysis.
- IPython Cookbook, Second Edition: A practical recipe book for IPython and Python.
- Automate the Boring Stuff with Python: An introductory book on automation with Python.
Statistics, Visualization, and Computer Science
- An Introduction to Statistical Learning: An introductory book on statistical learning.
- Fundamentals of Data Visualization: A book explaining core principles of data visualization. License: CC BY-NC-ND 4.0.
- Think Bayes 2: An introductory book on Bayesian statistics.
- Think Stats, 3rd edition: A book for learning statistics with Python.
- Foundations of Computer Vision: A book on the foundations of computer vision.
- Open Data Structures: An introductory book on data structures.