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 …


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。

Ensembl Genomic Reference in Bioconductor

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

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.