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 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 …

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 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 …

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 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 …

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 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 …

Coding 初學指南附錄 - Bioinfo Practices using Python

A walk through of practices created by Rosalind Team.

Plot Sequencing Depth with Gviz

TL;DR Plot exome sequencing depth and coverage with genome annotation using Gviz in R. Then apply detail control on Gviz annotation track displaying.

This is an extending post from Genomic Data Processing in Bioconductor, though I haven’t finished reading all the reference in that post. The background knowledge …

Overview of Genomic Data Processing in Bioconductor

Notes of fundamental tools and learning resources for handling genomic data in R with Bioconductor.

FASTA/Q sequence processing toolkit -- seqtk

This post demonstrates the FASTQ to FASTA conversion and sequence quality check using seqtk.