Store GDC genome as a Seqinfo object
Genomic Data Commons (GDC) hosted by NCI is the place to harmonize past and future genomic data, such as TCGA, TARGET, and CPTAC projects …
Build EnsDb from a local Ensembl MySQL database
In some occasions, I need to access the older version of Ensembl human transcripts. For example, the mutation calls generated by the NCI’s …
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.
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.