Yuan Blog

「仰望星空 脚踏实地」

updated RNAseq pipeline using nextflow

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Posted by Yuan on October 1, 2023

RNAseq update

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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

Rmarkdown chunk code options

Hide code, text output, messages, or plots

This blog is mainly from rmarkdown-cookbook/ and Yihui Xie’s Book Settings in chunk code 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 3...

Posted by Yuan on August 31, 2022

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一个在生物大数据领域耕耘的牛仔
A geeker working on big data in biology.

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