Steven Ge

Dealing with messy data in R: data cleaning and visualisation 8-10 April 2026

In many R courses, data are clean & everything just works.
But real life is messy—and that’s where problems start

👉 Our course with @cecibaldoni.bsky.social -Dealing with Messy Data in R in April: clean, join & visualise real datasets with tidyverse & ggplot2 💻📊
shorturl.at/zdmht
#Rstats #MessyData

A human pan-disease blood atlas of the circulating proteome | Science www.science.org/doi/10.1126...

Thanks Carlo! The students were great!

ragnar 0.3.0 The new release of ragnar adds faster ingestion, new embedding providers, improved retrieval, and new integrations for using ragnar stores from tools.

ragnar 0.3.0 is now on CRAN! 🚀 An R toolkit for RAG from your docs: faster ingestion, better retrieval, Azure OpenAI + Snowflake embeddings, and MCP serving. tidyverse.org/blog/2026/01...

#rstats #rag #ai

Grunya Sukhareva - Wikipedia

TIL: Before Hans Asperger or Leo Kanner, a Jewish-Ukrainian psychiatrist named Grunya Sukhareva defined autism in 1925. Both men did not cite her work. She also had documented how it affected women and girls, where the men did not.

en.wikipedia.org/wiki/Grunya_...

Issue 67: The PyDMD Project, Build a Text-to-Image Generator, New Tutorials A weekly curated update on data science and engineering topics and resources.

My weekly newsletter is out!

ramikrispin.substack.com/p/issue-67-t...

#python #ai #llm

Excited to share "Claude Code for Everyone"—a set of step-by-step, hands-on tutorials to help you put AI to work on your laptop. It isn’t just an AI coding tool for developers; it is a powerful local AI agent to support research, writing, editing, and more.

Check it out: gexijin.github.io/vibe/

Claude Code for Everyone

The following tutorial by Prof. Steven Ge (@stevenge.bsky.social ) provides a step-by-step guide for setting up and working with Claude Code. This includes different routes by OS (Mac and Windows) and programming languages ( #Rstats and #Python).

gexijin.github.io/vibe/

80-mer DNA aptamer as a selective marker for #Senescence
Targeting EDA-Fibronectin Kd 500~1000 pM

Label senescent cells in naturally aged🐭🫁
Aptamer binding ⬇️in 21-mo INK-ATTAC🐭 with p16 cells eliminated

#Aging_Cell 2025
onlinelibrary.wiley.com/doi/10.1111/...

What’s inside:
- Windows + Mac setup guides
- A clear learning path: Basics → R / Python
- Practical workflows with VS Code, Git, WSL (Windows), and Docker
- Real projects (e.g., using Claude Code to help write a research paper)
- Spanish, Chinese, and Japanese versions

Excited to share "Claude Code for Everyone"—a set of step-by-step, hands-on tutorials to help you put AI to work on your laptop. It isn’t just an AI coding tool for developers; it is a powerful local AI agent to support research, writing, editing, and more.

Check it out: gexijin.github.io/vibe/

Claude Code is more than coding. To prove it: here’s how I built ~100 tutorials in about a week by packaging my workflow into slash commands (reusable prompts)—write, review, and translate.

It automates workflows.

How I did it: gexijin.github.io/vibe/Buildin...
Tutorials: gexijin.github.io/vibe/

When plotting, LLMs see what they expect to see - Posit Data science agents need to accurately read plots even when the content contradicts their expectations. Our testing shows today's LLMs still struggle here.

To be effective, data science agents need to be able to read plots reliably. @sara-altman.bsky.social and I wrote about some concerning findings on LLMs' ability to interpret plots when the content contradicts their expectations on the @posit.co blog.

posit.co/blog/introdu...

GitHub - gexijin/vibe: Vibe coding via Claude Code & Codex Vibe coding via Claude Code & Codex. Contribute to gexijin/vibe development by creating an account on GitHub.

This is my R development setup — built on VS Code and running both Claude Code and OpenAI’s Codex inside a Docker container. It also supports Shiny apps and has been working great for me.

I am on Windows. These coding agents were initially designed for Linux, I think.

github.com/gexijin/vibe

The data is searchable on this site that the Renthal lab put together (thanks to Shams in Will's lab for leading this): painseq.shinyapps.io/u19humandrga...

New iDEP feature: instantly annotate k-means clusters with enriched pathways. Fewer clicks, better insights. Explore your data! Give it a spin on your RNA-seq data: bioinformatics.sdstate.edu/idep/

GitHub Copilot Chat in Positron Assistant 🤖

Positron Assistant now supports GitHub Copilot for both completions and chat!

Add GitHub Copilot as a model provider for access to its models, chat participants, and tools.

Learn more: positron.posit.co/assistant

Minimalist Async Evaluation Framework for R Designed for simplicity, a mirai evaluates an R expression asynchronously, locally or distributed over the network. Built on nanonext and NNG for modern networking and concurrency, scales efficiently ...

I put out a patch release of mirai today. Version 2.5.2 really improves the OpenTelemetry integration so you can more easily see into your async workflows. Other key ecosystem packages will roll out with this enabled - next up: Shiny!

mirai.r-lib.org

#Rstats

iDEP website: bioinformatics.sdstate.edu/idep/

YouTube video by Steven Ge Analyze RNA-Seq data with IDEP, an interactive website

In this video, I show how to use iDEP to interpret bulk RNA-seq data. Start with QC plots and exploratory analyses before identifying differentially exp. genes and pathways. We picked up on high mitochondrial rRNA counts, one male mixed in with 7 female mice.
www.youtube.com/watch?v=ta1o...

The Forecaster | Rami Krispin | Substack A newsletter about time series analysis and forecasting. Click to read The Forecaster, by Rami Krispin, a Substack publication with hundreds of subscribers.

I kicked off a new newsletter focused on time series analysis and forecasting.

My goal is to use it as both a framework and motivation to write my upcoming books on time series and forecasting.

If you are interested, please sign up here:
theforecaster.substack.com

#timeseries #rstats #python

letter from the statistics department chair at UNL

The Department of Statistics at the University of Nebraska–Lincoln is under threat of closure, with tenured faculty facing dismissal. This is a small but globally impactful department.
Please consider writing a letter of support. Your voice could make a real difference.

5 tools to visualize genomic datasets 🧵
1. Karyoploter bernatgel.github.io/karyoploter...

I had a 26GB TSV file. R choked. So I turned to UNIX. And it worked.
1/
You only need 500 columns.
But the file is 26GB.
R freezes. Memory bleeds.
You need the data—but you don’t need the pain.
Here’s what I did.

The Cagent Project, The Bayesian Data Analysis Book, Getting Started with Claude Code A weekly curated update on data science and engineering topics and resources.

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ramikrispin.substack.com/p/the-cagent...

The Snakemake Project, the AI Advantage Book, Claude Code Tutorials and More A weekly curated update on data science and engineering topics and resources.

My weekly newsletter is out!

ramikrispin.substack.com/p/the-snakem...

#llm #ai #python

Getting Started with Docker Model Runner Docker recently introduced a new feature for Docker Desktop — Docker Model Runner, which allows running and interacting with LLMs locally…

My Docker Model Runner tutorial is also available on Medium (for paid subscribers). Alternatively, for non-subscribers, it is open in my newsletter.

medium.com/data-science...

AIOps newsletter: theaiops.substack.com

#ai #docker #datascience

Understand NGS sequencing files
bioinf.comav.upv.es/courses/seq...

The PandasAI Project, Learning SQL Book, Fine-Tuning Local LLMs A weekly curated update on data science and engineering topics and resources.

My weekly newsletter is out!

This week:
🔹 Open Source of the Week - The PandasAI project
🔹 New learning resources
🔹 Book of the week - Learning SQL by Alan Beaulieu

📌 Join 30k subscribers and subscribe for weekly updates.

ramikrispin.substack.com/p/the-pandas...

#ai #python #datascience #sql

Hello #dataBS (& especially #TidyTuesday) fam! I'm trying to organize a thing to help me keep TidyTuesday running smoothly, but first I need to get a bit of a runway. Every week I curate a TT dataset, and it's wearing me down. Please see github.com/rfordatascie... for some ways you can help! #RStats