README.md

In biobricks: Access Data Dependencies Installed Through 'Biobricks.ai'

Here's a revised README that should offer a clearer and more direct explanation of your package and its functionality.

Biobricks R Package

The biobricks R package facilitates the management and use of bioinformatics databases, streamlining access to a range of datasets.

Installation

Step 1: Install the Python Package

pip install biobricks

Step 2: Install the R Package

install.packages('biobricks')

Quickstart

Setup the Command Line Tool

pip install biobricks
biobricks configure     # Set the BBLIB path and obtain a token
biobricks install clinvar  # Install a database of your choice

Install a Bioinformatics Database (Brick)

For example, to install the ClinVar database:

biobricks install clinvar

Asset Overview

To list the assets provided by a brick:

biobricks assets clinvar

Using ClinVar Assets in R

Load ClinVar assets, which are stored as Parquet files:

clinvar <- biobricks::bbassets('clinvar')
arrowds <- arrow::open_dataset(clinvar$allele_gene_parquet)
head(arrowds) %>% dplyr::collect()

Additional Documentation

For more details, visit docs.biobricks.ai.

Hope this suits your needs.

biobricks documentation built on Nov. 2, 2023, 5:07 p.m.