Software

I recommend pixi, a modern, fast environment and package manager for the Python ecosystem, in the place of anaconda and conda. pixi is cross-platform, supports both Python and R, resolves environments quickly, and uses the familiar conda-forge ecosystem for package sourcing. It also manages all dependencies—including binaries and libraries—making installation and environment reproduction seamless.

Older tools like anaconda and conda are still widely used, but pixi has a much smoother workflow and improved speed. Instead of heavy base installs (anaconda), you define lightweight, reproducible environments in a pixi.toml file. This ensures all your dependencies are explicit and portable.

A minimal example for a Python data analysis environment:

[project]
name = "myenv"

[dependencies]
python = "3.11"
jupyter = "*"
pandas = "*"
numpy = "*"
scipy = "*"
scikit-learn = "*"

You can also run program without installing them:

pixi run jupyter-console

Another neat trick is that you can use pixi-pack to build an environment on one machine and deploy it to another machine. That means no need for more complicated tools like docker.

These days much of the data you will want to analyze lives on the web. If you want to get this data you will run into terms like HTTP, FTP, REST APIs, JSON. If you want to work with these things you should probably learn curl.

The basic usage of curl is simple, yet endlessly customizable:

curl [options] [URL...]

Why curl over something like wget? curl by default writes to STDOUT, while wget writes directly to disk. This gives curl a significant advantage in being a flexible utility in between pipes.

Bonus tip: curl is available in conda-forge.

jq is like awk but specifically for json files. It is fast, flexible, and plays nicely with your other command-line tools.

It is extremely useful for pretty-printing your json files, and can be easily used to glob multiple files. The more advanced syntax including select/map can help you explore very complex files in just a few lines of code.

Bonus tip: jq is available in conda-forge.

xmlstarlet is like awk/sed/grep for XML files.

It is extremely useful for browsing the structure of your XML files (xmlstarlet el), and subsequently extract the relevant information (xmlstarlet sel). It is written in C so it is very fast.

Oftentimes you need to look through a csv file through the command line, and maybe you even want to do some basic analysis. Enter xan, which is written in Rust and is extremely fast and capable. xan can quickly filter, join, pretty print, etc. a csv, which makes it an invaluable tool.

I used to recommend csvkit which is written in python, but the performance of xan has convinced me to switch for good.

Rclone is a command-line tool for accessing data located in cloud storage, including common enterprise tools like Box, Dropbox, or Google Drive.

It’s fairly easy to use because it has commands that should be familiar to most unix users. Moreover, it is pretty fast.

It also happens to be installed by default on WRDS (/usr/bin/rclone).

GNU parallel is a great command line utility written in Perl which allows for very fine-tuned control over parallelization. If you are familiar with something like xargs, then parallel is like a more robust, scalable version of xargs.

Admittedly the learning curve for parallel can be a bit high, but it makes replacing serial loops with parallel tasks very easy.

Suppose you have a script SOMETHING which you want to run over a list of csv files in your current directory:

for i in $(find *.csv); do
    ./SOMETHING $i
done

One way to easily parallelize this in bash is to add &:

for i in $(find *.csv); do
    ./SOMETHING $i &
done

You could also accomplish the same task with a pipe:

find *.csv | ./SOMETHING

or if the number of csv files is large you can use xargs:

find *.csv | xargs ./SOMETHING

If you want more fine tuned control, such as over the number of concurrent jobs, then that is where parallel comes in:

find *.csv | parallel -j8 ./SOMETHING

parallel is very powerful, and can handle things like parsing arguments, and handle concurrent writing in a safe way. Suppose that your input is a pipe delimited file that you want to pass as arugments to your script and output to a single file:

cat INPUT.csv | parallel --colsep '\|' "./SOMETHING {1} {2}" > OUTPUT.csv

Just remember you bash quoting rules and you will be fine!

• bat which is like cat with syntax highlighting, making it perfect for quickly viewing code and data files.
• fd which is a simple, fast alternative to find with intuitive syntax like fd pattern instead of find . -name '*pattern*'.
• fzf for fuzzy finding stuff.
• exa which is like a more advanced ls.
• btop which is a prettier htop.
• ripgrep which is a very fast grep search from the developer of xsv.
• yazi which is a fast file manager.
• zoxide which is a more advanced cd.
• tspin which adds timestamps to piped output, useful for monitoring long-running computations.

• direnv automatically loads environment variables from .envrc files when you enter a directory. Essential for managing project-specific configurations without polluting your global environment. Just echo 'export API_KEY=foo' > .envrc && direnv allow.
• lazygit provides a terminal UI for git that makes complex operations intuitive. Perfect for researchers who want version control without memorizing git commands. Press ? for help on any screen.
• atuin replaces your shell history with a SQLite database, enabling powerful search across all your commands. Sync across machines and never lose that complex data processing pipeline again. Search with Ctrl-R.
• gh is GitHub’s official CLI for managing pull requests, issues, and repositories from the terminal. Clone with gh repo clone owner/repo, create PRs with gh pr create.

• claude code is an AI-powered coding assistant that helps with software development tasks. It can search codebases, write and edit files, run commands, and help debug issues, it can even read Jupyter Notebook files and “see” your images. The VSCod extension is also very nicely integrated, as it can automatically add the lines you select as context.
• gemini-cli is a free AI assistant powered by Google’s Gemini models. You can even have Claude Code call Gemini directly for real-time code reviews during development, creating an AI pair programming experience.

requests is a dead-simple HTTP library for python. Like curl it is an essential building tool for working with data that lives on the web (aka scraping).

For example, many websites are now built around REST APIs and deliver JSON payloads. Rather than scraping HTML with something like BeautifulSoup, lxml, or worst of all Selenium you can save yourself a lot of time and preserve your sanity by just using requests to get at the underlying data. All you need is the Inspect window of your browser, and some patience and soon you will be an API scraping master.

Bonus tip: https://curl.trillworks.com/ is a great website that converts curl statements into requests code. This is especially useful because some browsers allow you to copy the results of HTTP requests into curl, which you can easily convert into requests code!

asyncio is part of the python standard library as of python 3.4. It is a library for running concurrent (single-threaded) code, and brings python to the forefront of event-driven programming. That is a fancy way of saying that it is a neat library that can help you write highly parallel code, help you write your own network apps, or even write some pretty fancy scrapers.

asyncio has spawned its own ecosystem of libraries, such as aiohttp which is like a async version of requests, and aiofiles for dealing with the filesystem asynchronously.

You have data. You use python. If these conditions apply, then you should use pandas. The genius of pandas is that provides a DataFrame, an indexed, two-dimensional, potentially heterogeneous and hierarchical table of rows and columns. In all likelihood 99% of the data you analyze with statistical techniques will fit into the DataFrame structure, and pandas makes working with DataFrames a breeze with powerful functions for data serialization and transformation.

ujson stands for UltraJSON, which is an ultra fast JSON serializer written in C with python bindings. For most applications you can use it as a drop-in replacement for the default python json module, which is written in pure python and as such is slower.

benedict is a python dictionary subclass that makes navigating dictionaries in python a lot easier. In many ways it is like BeautifulSoup, which is very good at working with irregular or malformed HTML/XML data, but for python dictionaries, and JSON-like data. It is not as full-featured as many of the libraries on this list, but it can be very useful if you are working with irregular JSON data.

At first glance, numba seems like an odd choice for python users. The appeal of python is that it is an interpreted language, and hence does not need to be compiled to run. numba is a compiler for python code. However, it is an easy to use, just-in-time (JIT) compiler using the LLVM compiler library. That means that it can take very simple python and numpy code and turn it into LLVM compiled code that is nearly as fast as C or FORTRAN code.

A good use case for numba is taking an expensive matrix multiplication and re-writing it as a loop. This may seem counterintuitive as the whole point of numpy is to abstract away from slow python loops for optimized abstracted matrix operations. Yet these dumb, slow python loops combined with numba can be significantly faster than numpy counterparts if used correctly.

marimo is a reactive Python notebook that solves many pain points of traditional Jupyter notebooks. Unlike Jupyter, marimo notebooks are stored as pure Python files, making them git-friendly and importable as modules. The reactive execution model means cells automatically re-run when their dependencies change, eliminating the hidden state issues common in Jupyter. For researchers, this means more reproducible analyses and easier collaboration. Just run marimo edit notebook.py to start.

altair is a declarative visualization library built on Vega-Lite. Unlike matplotlib’s imperative style, altair uses a grammar of graphics approach that makes complex visualizations surprisingly simple. For researchers, this means publication-quality plots with minimal code. Just alt.Chart(df).mark_point().encode(x='x', y='y') for a basic scatter plot, with automatic type inference and interactivity.

polars is a lightning-fast DataFrame library that often outperforms pandas by 10-100x. Written in Rust, it features lazy evaluation, automatic query optimization, and excellent memory efficiency. For researchers working with large datasets, polars can process data that would crash pandas. The API is expressive: df.filter(pl.col('x') > 5).group_by('category').agg(pl.col('y').mean()).

tidyverse is a metapackage of data analysis tools for R. In many ways it is like the anaconda default installation in that it includes so many of the essentials. To get started analyzing data in a modern R setup you will likely need ggplot2, dplyr, stringr, and purrr just to name a few. All of these are part of tidyverse.

tidyverse also contains one of the most useful packages in any language: haven, which allows you to read SAS and Stata files. Look, we can all pretend like we don’t have co-authors that use these languages, or we can deal with it and use haven.

data.table is very fast, and has an intuitive syntax. It is certainly different from tidyverse::dplyr, but for those familiar with pandas, PyTable, or sql it may be more intuitive.

Bonus tip: DataCamp has a great cheat sheet for data.table.

felm and alpaca are R packages for linear/logistic regressions with high dimensional fixed effects and clustered standard errors. Both are available on CRAN, and are fairly well documented.

DuckDB is a SQL-style database with very convenient syntax for data analysis. It works very well with standard tabular data formats, and plays nicely with python. It is also very fast for analytic workflows, including read/write and processing data. One of the most useful features is the variety of built-in datatypes, such as LIST and STRUCT which map to python/JSON datatypes. It also allows for nested or composite datatypes, which are often found in real-world data. By default, DuckDB operates in-memory databases. In many ways, it is like SQLite but designed for data analysis workflows. It also features a lot of useful extensions whic facilitate full text search, JSON querying, reading/writing remote files over HTTP, and reading from Postgres/SQLite databases.

DuckDB now plays nicely with both python and R, and with their respective dataframes. It is also very very good at reading all sorts of common data files like csv, json, and parquet.

Sometimes the only way to get data is through traditional web scraping. Scraping is controversial and at the very least most websites have some sort of rate limiting or bot restrictions. Other websites are weirdly designed and require javascript rendering to be able to access content. ScrapingBee handles the former by providing headless instances that imitate a real Chrome browser, running through different proxies (including residential IP addresses) and the latter through custom javascript rendering. Thus, ScrapingBee makes scraping much much easier in the modern age.

Unlike the rest of the tools on this page, ScrapingBee is a service you have to pay for. But the rates are fairly reasonable considering that spinning up a custom solution (e.g., multiple AWS instances) is costly and time-consuming. Best of all ScrapingBee is fairly easy to use. If you can write a simple requests script (see above), then converting it to use ScrapingBee is trivial. Last but not least, ScrapingBee only charges you for successful requests, so if their proxies get blocked it doesn’t cost you any additional money.

Warning: If you pay for a higher tier with concurrency, do not follow the ScrapingBee tutorials and try to use multiprocessing or concurrent.futures for parallelism. Although it is syntactically simple, they run into the Python GIL and will lock after a few iterations. Instead, use aiohttp and just replace the url field with the ScrapingBee url, include your API Key as a parameter, and the url you want to scrape as another parameter.

• WezTerm / Ghostty are modern terminal emulators with GPU acceleration, split panes, and extensive customization. They also provide native image support.

• Superwhisper provides system-wide voice transcription using different transcription models. It is much better than the built-in Apple dictation, and can be much faster than typing. You can also have AI process your transcript directly, so you can for example, dictate some sentences and have it automatically turned into a properly formatted email.
• Homerow enables keyboard-only navigation of macOS by showing letter hints on clickable elements. Essential for reducing mouse usage during long coding or writing sessions.
• Bitwarden is an open-source password manager with excellent cross-platform support.

• Logseq / Obsidian are powerful note-taking apps with bidirectional linking. Logseq uses an outliner approach while Obsidian uses traditional markdown files. Both excel at building a personal knowledge graph for research.
• Sioyek is a PDF viewer designed specifically for research papers and technical documents. Features include smart jump for references, portals for keeping figures visible while reading, and a command palette for keyboard-driven navigation.
• Paperpile is a reference manager that integrates seamlessly with Google Docs and Microsoft Word. It automatically extracts metadata from PDFs, syncs across devices, and makes citation formatting painless. The Chrome extension adds papers from Google Scholar with one click.
• Readwise Reader is a read-later app designed for deep reading and annotation. It handles PDFs, web articles, newsletters, and even YouTube videos. The killer feature is its powerful highlighting system that syncs with note-taking apps like Logseq or Obsidian. It also has an MCP, so you can connect it with LLMs like Claude, which then knows everything you have read/highlighted and can help you surface relevant passages or citations.