List of packages that I care, categorized by package managers.

brew (macOS)

  1. aria2, because I torrent with aria2c command. It feels better.
  2. encfs, for encrypting top secret documents. Or use Cryptomator (easier?)
  3. findutils, because I need to use the gfind command sometimes.
  4. git, because it is newer & better than the xcode-shipped git,
  5. gnupg.
  6. htop.
  7. hugo, an SCG for blogging.
  8. media-info
  9. mkvtoolnix, for processing *.MKV files.
  10. openvpn.
  11. pngquant, for optimizing *.PNG image files.
  12. python3.
  13. rbenv, ruby, ruby-build, some Ruby stuff that I don't why I need them.
  14. speedtest-cli, required when traveling to assess my life situation.
  15. ssh-copy-id, because I like remote servers.
  16. vim.
  17. webp, but only Google Chrome supports this format as of now.
  18. wget.
  19. youtube-dl, for downloading YouTube videos.
  20. node, for using some Node-based applications like gtop.
  21. R, because I need to run some fancy-pancy statistics.
  22. Pandoc, a versatile document converter.
  23. cryfs, a replacement to the aging encfs for encrypting files with FUSE.


  1. gtop, a nice version for htop but with much less information.
  2. inliner, for downloading single HTML file. Run inliner > example.html.
  3. marked, for converting a .md markdown file to .html. Use marked -i -o output.html --gfm. Must include that --gfm option.
  4. gnomon by PayPal, a nice tool for checking how long a command would run, similar to the time function.


  1. mkdocs, an SCG for launching a documentation website.
  2. glances, like htop but better.
  3. jupyterlab, the brand new UI for iPython/Jupyter Notebook.
  4. subliminal (see on GitHub) to search for movie subtitles.
  5. pip-autoremove to remove a pip3 package along with its dependencies (clean install).

A short note on updating pip3 packages. There are two commands to accomplish this. The first alternative is cleaner.

# alternative 1
$ pip3 install --upgrade -r <( pip freeze )

# alternative 2
$ pip freeze > requirements.txt
$ pip3 install --upgrade -r requirements.txt
$ rm requirements.txt


  1. ggplot2, because it is a must when it comes to data visualization.
  2. bioconductor, because I need to do some bioinformatics.
  3. edgeR & DESeq2 for RNA-seq differential expression analysis.
  4. TinyTex for a modular TeX installation. This package lives within R, so that's great.
  5. installr to manage the R installation itself. Run R Console, then call install.R() function.

Scoop (Win10)

  1. coreutils, so I can use some popular Linux/Unix commands.
  2. hugo, an SCG for blogging.
  3. python, because why not (this installs python3).
  4. r, because I need to run some fancy-pancy statistics. Install official R binary is better, so that RStudio can find it.