Yuan Blog

Supply Chain Acharya - Data simulation details

Gen AI Capstone 2025Q1

A supply chain is only as strong as its weakest data point. Kaggle Notebook The Kaggle Notebook for this blogpost could be found at: Note: [Kaggle Notebook 1: Supply Chain Data Simulation]...

Posted by Sonney George, Hari Priya Ramamoorthy, Yuan Shang, Toshal Warke (Alphabetical Order) on April 14, 2025

Updated RNAseq Pipeline Using NextFlow

A modular, scalable, and reproducible workflow for RNA-seq data analysis with built-in QC, alignment, and quantification steps

🚀 Overview As RNA-Seq continues to be a core technology for transcriptomic analysis, having a reproducible, scalable, and modular pipeline is essential. In this post, I’ll walk through recent upd...

Posted by Yuan on October 1, 2023

RNAseq analysis pipline update

Building an RNA Seq Pipeline for Reproducible Research and Reporting

From Reads to Reports: RNA-Seq Unveiled The github repository for this blogpost (including codes and potential documents) could be found at: Note: [RNA Seq Analysis report generation pipeli...

Posted by Yuan on May 23, 2023

config of a xamp or xapp server

manually

I have used apache/tomcat-mysql-php many years ago. Recently, I need to configure my own local database management system, to manage EHR datasets based on OMOP schema. So, I picked this system up....

Posted by Yuan on November 8, 2022

Analyzing MIMIC dataset using various machine learning models

From data cleaning to model evaluation

屈身守分，以待天时，不可与命争也 To do ordinary bioscience, we need diligent grant reviwers with high social skills. To do good bioscience, we need heroes. Altough I did not finish genomics PRS part of ROSMA...

Posted by Yuan on October 13, 2022

Synchronize file from ROSMAP

synaspeclient and synapseutils

大丈夫处世，不能立功建业，不几与草木同腐乎？ Get accessing to data hold by Synpase is easy as long as you have the permission. Below is my script to download data from there, using Python scripts. I get all Syn_nu...

Posted by Yuan on October 10, 2022

Calculate SNP Heritability

Using SumHer

夫英雄者，胸怀大志，腹有良谋，有包藏宇宙之机，吞吐天地之志者也。 Taggings in heritability modeling All applications of SumHer require a tagging file, which records the (relative) expected heritability tagged by each predict...

Posted by Yuan on September 29, 2022

Construct a GWAS reference panel for AD

Choose base GWAS and Reference Panel

I did not mean to learn GWAS, but it happened. Heritability I wanted to calculate PRS for Alzheimer’s, following the tutorials I wrote in May,2022. However, the WGAS summary data I have lack ...

Posted by Yuan on September 27, 2022

git multiprofile settings

multithread roles

Time management Default git config file Git profile file is at ~/.gitconfig , which has a content like this: [credential] helper = cache [user] name = Yuan Shang email = shangyuan5000...

Posted by Yuan on September 21, 2022

Frequently Used Awk Commands

For fast text stream manipulations

运用之妙，存乎一心 Introduction Awk is a program that you can use to select particular records in a file and perform operations upon them. It is installed on Linux and Mac by default. Awk is an inter...

Posted by Yuan on September 16, 2022