Steven Ge
@stevenge.bsky.social
Professor, founder of Orditus. AI, genomics, bioinformatics
Reposted by Steven Ge
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...
posit.co/blog/introdu...
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.
posit.co
November 13, 2025 at 3:07 PM
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...
posit.co/blog/introdu...
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
I am on Windows. These coding agents were initially designed for Linux, I think.
github.com/gexijin/vibe
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.
github.com
November 10, 2025 at 6:25 PM
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
I am on Windows. These coding agents were initially designed for Linux, I think.
github.com/gexijin/vibe
Reposted by Steven Ge
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...
NIH PRECISION Human Pain Network DRG Atlas
painseq.shinyapps.io
November 7, 2025 at 5:45 PM
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/
November 6, 2025 at 2:54 AM
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/
Reposted by Steven Ge
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
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
November 5, 2025 at 4:20 PM
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
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
Reposted by Steven Ge
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
mirai.r-lib.org
#Rstats
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 ...
mirai.r-lib.org
November 5, 2025 at 10:37 PM
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
mirai.r-lib.org
#Rstats
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...
www.youtube.com/watch?v=ta1o...
Analyze RNA-Seq data with IDEP, an interactive website
YouTube video by Steven Ge
www.youtube.com
October 30, 2025 at 12:56 AM
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...
www.youtube.com/watch?v=ta1o...
Reposted by Steven Ge
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
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
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.
theforecaster.substack.com
October 13, 2025 at 12:51 AM
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
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
Reposted by Steven Ge
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.
Please consider writing a letter of support. Your voice could make a real difference.
September 19, 2025 at 4:28 AM
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.
Please consider writing a letter of support. Your voice could make a real difference.
Reposted by Steven Ge
5 tools to visualize genomic datasets 🧵
1. Karyoploter bernatgel.github.io/karyoploter...
1. Karyoploter bernatgel.github.io/karyoploter...
September 17, 2025 at 1:15 PM
5 tools to visualize genomic datasets 🧵
1. Karyoploter bernatgel.github.io/karyoploter...
1. Karyoploter bernatgel.github.io/karyoploter...
Reposted by Steven Ge
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.
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.
September 16, 2025 at 1:45 PM
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.
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.
Reposted by Steven Ge
Reposted by Steven Ge
Reposted by Steven Ge
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
medium.com/data-science...
AIOps newsletter: theaiops.substack.com
#ai #docker #datascience
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…
medium.com
August 27, 2025 at 10:32 PM
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
medium.com/data-science...
AIOps newsletter: theaiops.substack.com
#ai #docker #datascience
Reposted by Steven Ge
Understand NGS sequencing files
bioinf.comav.upv.es/courses/seq...
bioinf.comav.upv.es/courses/seq...
August 28, 2025 at 1:45 PM
Understand NGS sequencing files
bioinf.comav.upv.es/courses/seq...
bioinf.comav.upv.es/courses/seq...
Reposted by Steven Ge
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
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
The PandasAI Project, Learning SQL Book, Fine-Tuning Local LLMs
A weekly curated update on data science and engineering topics and resources.
ramikrispin.substack.com
August 23, 2025 at 2:22 PM
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
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
Reposted by Steven Ge
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
August 15, 2025 at 11:23 AM
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
Reposted by Steven Ge
Life-saving idea! Pass it on!
August 5, 2025 at 11:16 PM
Life-saving idea! Pass it on!
Reposted by Steven Ge
My weekly newsletter is out!
This week's agenda:
🛠️ The social-media-kit project
📝 New learning resources
📚Book of the week - Models Demystified by Michael Clark and Seth Berry
📌 Join 30k subscribers and subscribe for weekly updates.
ramikrispin.substack.com/p/new-book-m...
#datascience #ai
This week's agenda:
🛠️ The social-media-kit project
📝 New learning resources
📚Book of the week - Models Demystified by Michael Clark and Seth Berry
📌 Join 30k subscribers and subscribe for weekly updates.
ramikrispin.substack.com/p/new-book-m...
#datascience #ai
August 2, 2025 at 2:14 PM
My weekly newsletter is out!
This week's agenda:
🛠️ The social-media-kit project
📝 New learning resources
📚Book of the week - Models Demystified by Michael Clark and Seth Berry
📌 Join 30k subscribers and subscribe for weekly updates.
ramikrispin.substack.com/p/new-book-m...
#datascience #ai
This week's agenda:
🛠️ The social-media-kit project
📝 New learning resources
📚Book of the week - Models Demystified by Michael Clark and Seth Berry
📌 Join 30k subscribers and subscribe for weekly updates.
ramikrispin.substack.com/p/new-book-m...
#datascience #ai
Reposted by Steven Ge
I NEED to tell you the story of Tae Heung “William” Kim.
He's a graduate student at Texas A&M where he's working on a vaccine for Lyme disease.
He's a *legal permanent resident* of the United States.
And he's been in ICE detention for 12 days & counting, transferred Tuesday to South Texas.
He's a graduate student at Texas A&M where he's working on a vaccine for Lyme disease.
He's a *legal permanent resident* of the United States.
And he's been in ICE detention for 12 days & counting, transferred Tuesday to South Texas.
July 31, 2025 at 11:35 AM
I NEED to tell you the story of Tae Heung “William” Kim.
He's a graduate student at Texas A&M where he's working on a vaccine for Lyme disease.
He's a *legal permanent resident* of the United States.
And he's been in ICE detention for 12 days & counting, transferred Tuesday to South Texas.
He's a graduate student at Texas A&M where he's working on a vaccine for Lyme disease.
He's a *legal permanent resident* of the United States.
And he's been in ICE detention for 12 days & counting, transferred Tuesday to South Texas.
Reposted by Steven Ge
Flossie Wong-Staal (1946 – 2020) was a Chinese-American virologist and molecular biologist.
She was the first scientist to clone HIV and determine the function of its genes, which was a major step in proving that HIV is the cause of AIDS.
🔬🧪 #WomenInSTEM
She was the first scientist to clone HIV and determine the function of its genes, which was a major step in proving that HIV is the cause of AIDS.
🔬🧪 #WomenInSTEM
July 25, 2025 at 7:36 PM
Flossie Wong-Staal (1946 – 2020) was a Chinese-American virologist and molecular biologist.
She was the first scientist to clone HIV and determine the function of its genes, which was a major step in proving that HIV is the cause of AIDS.
🔬🧪 #WomenInSTEM
She was the first scientist to clone HIV and determine the function of its genes, which was a major step in proving that HIV is the cause of AIDS.
🔬🧪 #WomenInSTEM
I will present on AI-powered data science platforms on Monday, July 21, at 11 am EST at the Univ of Virginia. Zoom link:
kohl.aaec.vt.edu/events/data-...
kohl.aaec.vt.edu/events/data-...
Virtual Speaker Series: Data Science Tools in Action
Join us at the Kohl Centre at Virginia Tech for a dynamic speaker series showcasing cutting-edge data science tools and their real-world applications. This series aims to make modern analytics more ac...
kohl.aaec.vt.edu
July 20, 2025 at 4:00 AM
I will present on AI-powered data science platforms on Monday, July 21, at 11 am EST at the Univ of Virginia. Zoom link:
kohl.aaec.vt.edu/events/data-...
kohl.aaec.vt.edu/events/data-...
Reposted by Steven Ge
Orbital - new OSS from Posit, looks super practical application for ML pipelines 👇🏼
posit.co/blog/introdu...
#python #rstats #datascience
posit.co/blog/introdu...
#python #rstats #datascience
Posit
Orbital is a new library that converts Scikit-learn pipelines into SQL queries, enabling machine learning model inference directly within SQL databases.
posit.co
July 17, 2025 at 4:27 AM
Orbital - new OSS from Posit, looks super practical application for ML pipelines 👇🏼
posit.co/blog/introdu...
#python #rstats #datascience
posit.co/blog/introdu...
#python #rstats #datascience
Reposted by Steven Ge
New blog post: @posit.co Positron Assistant provides inline completions with GitHub Copilot and chat/agent using Claude 4 Sonnet. Demo: using agent mode to create an #Rstats package with Roxygen2 docs and testthat unit tests. doi.org/10.59350/gkj...
July 16, 2025 at 10:22 AM
New blog post: @posit.co Positron Assistant provides inline completions with GitHub Copilot and chat/agent using Claude 4 Sonnet. Demo: using agent mode to create an #Rstats package with Roxygen2 docs and testthat unit tests. doi.org/10.59350/gkj...
Reposted by Steven Ge
🚨 BREAKING 🚨 The National Science Foundation has sent an email out to its members to collect signatures for a dissent declaration similar to the NIH’s Bethesda Declaration and the EPA’s Declaration of Dissent.
This comes on the heels of Lee Zeldin putting 139 EPA declaration signers on admin leave
This comes on the heels of Lee Zeldin putting 139 EPA declaration signers on admin leave
July 10, 2025 at 1:21 AM
🚨 BREAKING 🚨 The National Science Foundation has sent an email out to its members to collect signatures for a dissent declaration similar to the NIH’s Bethesda Declaration and the EPA’s Declaration of Dissent.
This comes on the heels of Lee Zeldin putting 139 EPA declaration signers on admin leave
This comes on the heels of Lee Zeldin putting 139 EPA declaration signers on admin leave