Python

Paired Ends Wrapped: Top 10 Posts From 2025

R + AI, uv, RAG+Zotero, Quarto books, Codex in Positron, Positron assistant & copilot, academia to biotech, RAG in R with ragnar, genome engineering…

Jan 5 • Stephen Turner

Scikit-bio: Python for Omics

The "missing middle" for omics data analysis in Python

Dec 16, 2025 • Stephen Turner

Weekly Recap (Nov 21, 2025)

R updates (R Data Scientist, R weekly)

Nov 21, 2025 • Stephen Turner

Weekly Recap (Nov 14, 2025)

posit::conf(2025) & Nextflow Summit talks, bioRxiv+medRxiv AI reviews, R updates (R Data Scientist, R weekly), Claude Scientific Skills, Python package…

Nov 14, 2025 • Stephen Turner

posit::conf(2025) talks on YouTube

Over 100 recorded talks from posit::conf(2025) are now available on YouTube

Nov 10, 2025 • Stephen Turner

Closing my tabs (Sep 5 2025)

NIH budget, AI, R, Bluesky & Science, state of biotech, AI in higher ed, R packages Top 40, structural variation, statistical power, Python documentary…

Sep 5, 2025 • Stephen Turner

uv, part 4: uv with Jupyter

Using uv with Jupyter: demo using polars and seaborn for analysis and visualization.

Jun 23, 2025 • Stephen Turner

uv, part 3: Python in R with reticulate

Two demos using Python in R via reticulate+uv: (1) Hugging Face transformers for sentiment analysis, (2) pyBigWig to query a BigWig file and visualize…

May 6, 2025 • Stephen Turner

uv, part 2: building and publishing packages

Using uv to create, manage, build, and publish a Python package to PyPI

Mar 24, 2025 • Stephen Turner

uv, part 1: running scripts and tools

Over the past year I’ve heard a lot great things about uv, an extremely fast Python package and project manager, written in Rust.

Mar 3, 2025 • Stephen Turner

Turn a GitHub repo into a single text file for LLM-friendly input

The open source repo2txt web app will take a GitHub repo URL, displays the directory structure, lets you choose which files to include, and provides a…

Dec 9, 2024 • Stephen Turner

TIL: dplyr::mutate()'s .keep argument

Use the .keep argument in dplyr::mutate() to control which variables to retain after mutating to create new variables.

Dec 2, 2024 • Stephen Turner

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