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Posts
GA Tech OMSCS Machine Learning for Trading (ML4T) Course Review
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I. Overall Impression
This was the first course I took in my OMSCS journey (Spring 2026), and overall I found it to be a very good introductory course to ease students into the program. The concepts taught are themselves not particulary difficult, but the constant deadlines for quizzes, projects, and exams give students a good sense of the expected pace in graduate school and prepare them for the more difficult courses to come. Read moreBridging R and Python in Bioinformatics: A Practical Setup with rpy2, uv, and mamba in Jupyter Notebooks
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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
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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
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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
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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
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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
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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?
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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 moreUsing GEOparse package to download NGS data
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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
One day I will post something…
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Perhaps on bioinformatics, general learnings, and on my travels…. Read more
portfolio
Replicating ‘Decoding aging in the heart via single cell dual omics of non-cardiomyocytes’ in Python 🐍
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Replicating single-cell RNA-seq and ATAC-seq analyses from a 2024 aging heart study, translated from R (Seurat/Signac) to Python using the scverse ecosystem (Scanpy, muon). Read more
MAGNET - Macrophage Annotation of Gene Network Enrichment Tool 🧲
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An interactive web application for performing enrichment analyses on gene sets specifically relevant to macrophages. Read more
Miniranger - a lightweight nextflow pipeline for processing scRNA-seq data 🔧
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A lightweight Nextflow pipeline for processing scRNA-seq data via simpleaf and the alevin-fry ecosystem. Takes FASTQ files and produces a cell × gene expression matrix and QC report. Read more
🔮 scOracle: An AI Assistant for Single-Cell Analysis
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A RAG-powered chatbot for single-cell analysis, grounded in real package documentation from Scanpy and Seurat to deliver accurate, domain-specific insights. Read more
publications
Paper Title Number 1
Published in Journal 1, 2009
This paper is about the number 1. The number 2 is left for future work. Read more
Recommended citation: Your Name, You. (2009). "Paper Title Number 1." Journal 1. 1(1).
Download Paper | Download Slides
Paper Title Number 2
Published in Journal 1, 2010
This paper is about the number 2. The number 3 is left for future work. Read more
Recommended citation: Your Name, You. (2010). "Paper Title Number 2." Journal 1. 1(2).
Download Paper | Download Slides
Paper Title Number 3
Published in Journal 1, 2015
This paper is about the number 3. The number 4 is left for future work. Read more
Recommended citation: Your Name, You. (2015). "Paper Title Number 3." Journal 1. 1(3).
Download Paper | Download Slides
Paper Title Number 4
Published in GitHub Journal of Bugs, 2024
This paper is about fixing template issue #693. Read more
Recommended citation: Your Name, You. (2024). "Paper Title Number 3." GitHub Journal of Bugs. 1(3).
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talks
Talk 1 on Relevant Topic in Your Field
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This is a description of your talk, which is a markdown file that can be all markdown-ified like any other post. Yay markdown! Read more
Conference Proceeding talk 3 on Relevant Topic in Your Field
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This is a description of your conference proceedings talk, note the different field in type. You can put anything in this field. Read more
teaching
Teaching experience 1
Undergraduate course, University 1, Department, 2014
This is a description of a teaching experience. You can use markdown like any other post. Read more
Teaching experience 2
Workshop, University 1, Department, 2015
This is a description of a teaching experience. You can use markdown like any other post. Read more