biodatalake ducklake example

getting_started.md

Connecting

Start duckdb, either on the command line or in R, etc. To connect to and then use the biodatalake ducklake, do the following inside the duckdb connection:

install httpfs;
load httpfs;
.read 'https://store.cancerdatasci.org/ducklake_config/ducklake_ro_connect.sql'

Querying

It can be helpful to start a duckdb UI at this point to see what tables are available:

call start_ui();

BugSigDB Exports

To take a look at the raw(ish) bugsigdb_export table:

select * from bronze.bugsigdb__export;

SRA metadata

select * from bronze.sra__studies limit 100;
select count(*), study_type from bronze.sra__studies group by study_type order by count(*) desc;