I have been using ensembldb to query genome annotations locally, which stores the Ensembl annotations in a offline SQLite database. By replacing the database engine with DuckDB, genome-wide queries are faster with small impact on gene specific queries (depending on the usage). DuckDB database’s file size is also smaller, and it can be even smaller by offloading the tables to external Parquet files.
Genomic Data Commons (GDC) hosted by NCI is the place to harmonize past and future genomic data, such as TCGA, TARGET, and CPTAC projects. GDC has its own genome reference, GRCh38.d1.vd1, which has 2,779 “chromosomes” including decoys and virus sequences. That said, the canonical chromosomes of GRCh38 …
In some occasions, I need to access the older version of Ensembl human transcripts. For example, the mutation calls generated by the NCI’s Genomic Data Common pipeline are annotated by Ensembl v84. To programmatically query the Ensembl annotations, I use the EnsDb SQLite database created by ensembldb, which is …
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.
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.
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 …
Notes of fundamental tools and learning resources for handling genomic data in R with Bioconductor.