I am transiting my GPG key again. However, for this time, I expect to use the new GPG master key longer and will start building this identity unless there is a concern about the key strength or I accidentally lose the key.
Back in my GPG key transition in 2016 …
Recently, I had to access gene annotations in multiple versions from multiple sources such as Ensembl, GENCODE, and UCSC. I used to rely on the R/Bioconductor ecosystem to query the coordinates of a gene annotation. There are existing Bioconductor packages ready for Ensembl and UCSC annotations (more info in …
UniProt Knowledge Base (UniProtKB) provides various methods to access their data. I settled on their XML format since no additional parsing code is required and the format is well defined, which comes with a schema. Plus, it turns out that databases such as PDB also provide their data export in …
Recently I’ve found that bioinformatic analysis in a database is not hard at all and the database set up wasn’t as daunting as it sounds, especially when the data are tabular. I used to start my analysis with loading everything into R or Python, and then figuring out …
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.
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 even across machines.
Snakemake has been my favorite workflow management system for a while. I came across it while writing my master thesis and from the …
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。
For my daily terminal life, I use fish shell. Fish shell can be largely described by the headline on its official website:
Finally, a command line shell for the 90s
fish is a smart and user-friendly command line shell for macOS, Linux, and the rest of the family.
Among all …
I started using GPG key as one of my small experiments in March, 2015. Throughout the setup, I made some mistakes, which I revoked later, and explored several usage scenarios. Although like what was said in the post I’m giving up on PGP, I don’t really use the …
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 …