GPG Key Transition

I am transiting my GPG key again. However, for this time, I expect to use the new GPG master key longer and will start …

Access gene annotation using gffutils

Recently, I had to access gene annotations in multiple versions from multiple sources such as Ensembl, GENCODE, and UCSC. I used to rely on …

Read UniProtKB in XML format

UniProt Knowledge Base (UniProtKB) provides various methods to access their data. I settled on their XML format since no additional parsing code is required …

Ad hoc bioinformatic analysis in database

Recently I’ve found that bioinformatic analysis in a database is not hard at all and the database set up wasn’t as daunting …

Using EnsDb's annotation database in Python

How to find and download the EnsDb, the Ensembl genomic annotation in SQLite database made by R package ensembldb, and use it in Python application.

Use Snakemake on Google cloud

TL;DR Run a RNA-seq pipeline using Snakemake locally and later port it to Google Cloud. Snakemake can parallelize jobs of a pipeline and …

Variants、eQTL、MPRA

本文內容主要來自 Barak Cohen 教授給的數堂課的筆記,以 Systems Biology 的角度來看 coding/noncoding variant modeling 和相關實驗 MPRA。

Changing login shell without chsh

For my daily terminal life, I use fish shell. Fish shell can be largely described by the headline on its official website:

Finally, a …

GPG Key Transition

I started using GPG key as one of my small experiments in March, 2015. Throughout the setup, I made some mistakes, which I revoked …

St. Louis PhD 生活

不知不覺,距離上篇文章已經 4 個月。這 4 個月裡,擔任 PyCon TW 2016 工作人員、寫完碩士論文、從一個讀了 7 年的學校畢業、然後前往美國的 Washington University in St. Louis …