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 …

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 …

Ensembl Genomic Reference in Bioconductor

Using fundamental R/Biocondcutor packages (e.g. AnnotationHub, ensembldb and biomaRt) to query Ensembl genomic references or annotations.

Add code block language name into CSS classes in Pelican Markdown

I used Pelican and its Markdown plugin to render blog post.

Recently I was playing with the Python Official Documentation, which has a decent …