Liang-Bo Wang's Blog

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 …

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 …

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

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

Recently I was playing with the Python Official Documentation, which has a decent code syntax highlighter powered by Pygments.

What’s more, the output of code examples can be toggled. That is, a code example:

>>> print('Hello World')
Hello …