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 …

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 …

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.