Author: Anup Jonchhe (anup@broadinstitute.org)
cmapBQ allows for targeted retrieval of relevant gene expression data
from the resources provided by The Broad Institute and LINCS Project hosted on Google BigQuery.
cmapBQ is available to install through pip with the command:
pip install cmapBQ or pip install --upgrade cmapBQ
to get the latest version.
A Google Cloud Account is necessary to run jobs on BigQuery to retrieve data. A setup guide for obtaining the required JSON credentials key can be found below:
https://cmapbq.readthedocs.io/en/latest/setup-guide.html
The service account credentials should be placed in the ~/.cmapBQ folder
and the ~/.cmapBQ/config.txt file should be edited such that the
credentials option points to the path of the service account credentials:
credentials: /path/to/service-credentials.json
Alternatively, the following command can be run from within a python session after installation. This only needs to be run once
import cmapBQ.query as cmap_query
import cmapBQ.config as cmap_config
cmap_config.setup_credentials(path_to_json)
##Tutorials and Documentation
A demo of cmapBQ functionality is available at this Github repo
and accessible through Colab:
Documentation is available on ReadTheDocs here: https://cmapbq.readthedocs.io