Posts by Tags

bioinformatics

Bridging R and Python in Bioinformatics: A Practical Setup with rpy2, uv, and mamba in Jupyter Notebooks

1 minute read

Published: June 28, 2025

When doing bioinformatics analysis using a Python workstack, it is quite common that crucial software packages are implemented only in R. Read more

Building a RAG-Powered AI Chatbot for Single-Cell Analysis - Part 5: Scaling Up & Cloud hosting

2 minute read

Published: May 07, 2025

In this post, I will push scOracle to the cloud, making it fully accesible via a browser-based interface. Read more

Building a RAG-Powered AI Chatbot for Single-Cell Analysis - Part 4: Streamlit UI

2 minute read

Published: May 04, 2025

In this post, I will transform the comand-line version of scOracle into a fully interactive chatbot by creating a clean, browser-based interface using Streamlit. Read more

Building a RAG-Powered AI Chatbot for Single-Cell Analysis - Part 3: CLI Query Engine

2 minute read

Published: May 03, 2025

In this part, we will connect the knowledge base we built in part 2 with an OpenAI LLM, transforming scOracle into a functional AI-powered chatbot for single-cell analysis! Read more

Building a RAG-Powered AI Chatbot for Single-Cell Analysis - Part 2: Data Ingestion & Indexing

4 minute read

Published: May 02, 2025

Download Scanpy source code & documentation

For a minimum viable product (MVP), I limited document ingestion to Scanpy, a leading Python-based framework for analyzing scRNA-seq data. Read more

Building a RAG-Powered AI Chatbot for Single-Cell Analysis - Part 1: Foundations

1 minute read

Published: April 29, 2025

Motivation

AI applications like ChatGPT have acted as capable personal assistants during my single-cell analysis projects, whether helping me debug a Scanpy error at midnight or brainstorming strategies for integrating scRNA and scATAC-seq data. Read more

How to deal with OOM when merging adata objects in Scanpy?

2 minute read

Published: March 19, 2025

Background

I was analyzing a scRNA-seq dataset that requires merging multiple adata objects. Normally, this would involve a simple call of anndata.concat. Read more

Using GEOparse package to download NGS data

1 minute read

Published: March 17, 2025

I used the Python package GEOparse to access and download data from GSE277702. This was part of my effort to replicate analyses from a manuscript on aging in the heart. Read more

datascience

Bridging R and Python in Bioinformatics: A Practical Setup with rpy2, uv, and mamba in Jupyter Notebooks

1 minute read

Published: June 28, 2025

When doing bioinformatics analysis using a Python workstack, it is quite common that crucial software packages are implemented only in R. Read more

general

One day I will post something…

less than 1 minute read

Published: February 14, 2025

Perhaps on bioinformatics, general learnings, and on my travels…. Read more

ml/ai

Building a RAG-Powered AI Chatbot for Single-Cell Analysis - Part 5: Scaling Up & Cloud hosting

2 minute read

Published: May 07, 2025

In this post, I will push scOracle to the cloud, making it fully accesible via a browser-based interface. Read more

Building a RAG-Powered AI Chatbot for Single-Cell Analysis - Part 4: Streamlit UI

2 minute read

Published: May 04, 2025

In this post, I will transform the comand-line version of scOracle into a fully interactive chatbot by creating a clean, browser-based interface using Streamlit. Read more

Building a RAG-Powered AI Chatbot for Single-Cell Analysis - Part 3: CLI Query Engine

2 minute read

Published: May 03, 2025

In this part, we will connect the knowledge base we built in part 2 with an OpenAI LLM, transforming scOracle into a functional AI-powered chatbot for single-cell analysis! Read more

Building a RAG-Powered AI Chatbot for Single-Cell Analysis - Part 2: Data Ingestion & Indexing

4 minute read

Published: May 02, 2025

Download Scanpy source code & documentation

For a minimum viable product (MVP), I limited document ingestion to Scanpy, a leading Python-based framework for analyzing scRNA-seq data. Read more

Building a RAG-Powered AI Chatbot for Single-Cell Analysis - Part 1: Foundations

1 minute read

Published: April 29, 2025

Motivation

rag

Building a RAG-Powered AI Chatbot for Single-Cell Analysis - Part 5: Scaling Up & Cloud hosting

2 minute read

Published: May 07, 2025

In this post, I will push scOracle to the cloud, making it fully accesible via a browser-based interface. Read more

Building a RAG-Powered AI Chatbot for Single-Cell Analysis - Part 4: Streamlit UI

2 minute read

Published: May 04, 2025

In this post, I will transform the comand-line version of scOracle into a fully interactive chatbot by creating a clean, browser-based interface using Streamlit. Read more

Building a RAG-Powered AI Chatbot for Single-Cell Analysis - Part 3: CLI Query Engine

2 minute read

Published: May 03, 2025

In this part, we will connect the knowledge base we built in part 2 with an OpenAI LLM, transforming scOracle into a functional AI-powered chatbot for single-cell analysis! Read more

Building a RAG-Powered AI Chatbot for Single-Cell Analysis - Part 2: Data Ingestion & Indexing

4 minute read

Published: May 02, 2025

Download Scanpy source code & documentation

For a minimum viable product (MVP), I limited document ingestion to Scanpy, a leading Python-based framework for analyzing scRNA-seq data. Read more

Building a RAG-Powered AI Chatbot for Single-Cell Analysis - Part 1: Foundations

1 minute read

Published: April 29, 2025

Motivation

single-cell

Building a RAG-Powered AI Chatbot for Single-Cell Analysis - Part 5: Scaling Up & Cloud hosting

2 minute read

Published: May 07, 2025

In this post, I will push scOracle to the cloud, making it fully accesible via a browser-based interface. Read more

Building a RAG-Powered AI Chatbot for Single-Cell Analysis - Part 4: Streamlit UI

2 minute read

Published: May 04, 2025

In this post, I will transform the comand-line version of scOracle into a fully interactive chatbot by creating a clean, browser-based interface using Streamlit. Read more

Building a RAG-Powered AI Chatbot for Single-Cell Analysis - Part 3: CLI Query Engine

2 minute read

Published: May 03, 2025

In this part, we will connect the knowledge base we built in part 2 with an OpenAI LLM, transforming scOracle into a functional AI-powered chatbot for single-cell analysis! Read more

Building a RAG-Powered AI Chatbot for Single-Cell Analysis - Part 2: Data Ingestion & Indexing

4 minute read

Published: May 02, 2025

Download Scanpy source code & documentation

For a minimum viable product (MVP), I limited document ingestion to Scanpy, a leading Python-based framework for analyzing scRNA-seq data. Read more

Building a RAG-Powered AI Chatbot for Single-Cell Analysis - Part 1: Foundations

1 minute read

Published: April 29, 2025

Motivation

How to deal with OOM when merging adata objects in Scanpy?

2 minute read

Published: March 19, 2025

Background

I was analyzing a scRNA-seq dataset that requires merging multiple adata objects. Normally, this would involve a simple call of anndata.concat. Read more

Sam Chen

Posts by Tags

bioinformatics

Download Scanpy source code & documentation

Motivation

Background

datascience

general

ml/ai

Download Scanpy source code & documentation

Motivation

rag

Download Scanpy source code & documentation

Motivation

single-cell

Download Scanpy source code & documentation

Motivation

Background