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 …
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。
Using fundamental R/Biocondcutor packages (e.g. AnnotationHub, ensembldb and biomaRt) to query Ensembl genomic references or annotations.
TL;DR Plot exome sequencing depth and coverage with genome annotation using Gviz in R. Then apply detail control on Gviz annotation track displaying …
Notes of fundamental tools and learning resources for handling genomic data in R with Bioconductor.
This post demonstrates the FASTQ to FASTA conversion and sequence quality check using seqtk.