Python on Badran Elshenawy

From Tidyverse to Scverse – Post 7: GlassBox UMAP — Making Dimensionality Reduction Interpretable

Mon, 25 May 2026 09:00:00 +0000

Your pipeline is fast and reproducible. But the UMAP step is still a black box. GlassBox UMAP changes that.

Lockfiles – Post 2: uv.lock vs renv.lock in Practice

Sat, 23 May 2026 09:00:00 +0000

Both Python and R have lockfiles, but they do not work the same way. Here is the practical difference between uv.lock, renv.lock, and the newer R tools closing the gap.

Lockfiles – Post 1: The Reproducibility Layer You're Probably Missing

Mon, 18 May 2026 09:00:00 +0000

Your code is on GitHub, your README is clean, and your pipeline worked perfectly six months ago. Here is why lockfiles are the missing piece.

From Tidyverse to Scverse – Post 6: Scanpy Done Right — The Modern PBMC 3k Pipeline

Thu, 07 May 2026 09:00:00 +0000

Every tool from this series — Polars, uv, Marimo, and now Plotnine — converge in a real scRNA-seq pipeline. Clone it, run it, make it yours.

From Tidyverse to Scverse – Post 5: marimo: The Notebook That's Actually a .py File

Wed, 06 May 2026 09:00:00 +0000

marimo stores notebooks as .py files — not JSON. Reactive, reproducible, git-friendly, and the most LLM-compatible notebook format available.

From Tidyverse to Scverse – Post 4: qmd vs ipynb: Why Quarto Notebooks Are the Future

Sun, 03 May 2026 09:00:00 +0000

Jupyter notebooks are JSON with embedded images. Quarto notebooks are plain text. For version control, LLMs, and reproducibility, qmd wins.

From Tidyverse to Scverse – Post 3: uv vs conda: Package Management That Finally Just Works

Fri, 01 May 2026 09:00:00 +0000

conda made you hate Python before you even started coding. uv fixes it: 10-100x faster installs, deterministic environments, and zero confusion.

From Tidyverse to Scverse – Post 2: Polars vs Pandas for Tidyverse Users

Tue, 28 Apr 2026 09:00:00 +0000

Pandas felt wrong after dplyr? Polars fixes almost everything: method chaining, lazy evaluation, and syntax that reads like tidyverse pipes.

From Tidyverse to Scverse – Post 1: Why I'm Making the Switch to Python

Fri, 24 Apr 2026 09:00:00 +0000

After 33 posts in R and building my own package, I’m adding Python to the toolkit. Here’s why — and what’s coming next.

Advanced scRNA-seq for Biologists – Post 4: RNA Velocity with scVelo

Mon, 13 Apr 2026 09:00:00 +0000

Pseudotime shows position. Velocity shows direction. Add arrows to your trajectory map with scVelo.