BiocOpenCRAVAT

Annotation of DNA variants is a crucial and dynamic field in human disease genetics. The OpenCRAVAT system organizes over 170 ‘annotators’ that resolve queries on features of genetic variants.

The BiocOpenCRAVAT workspace/workshop materials define interfaces between Bioconductor data structures and functions and the OpenCRAVAT system, to simplify the use of OpenCRAVAT annotation by Bioconductor users, and to simplify aspects of adding new annotation resources to OpenCRAVAT.

• Hit the Get started button to see an interactive catalog of available annotators and converters …
• See the Articles button for additional documents on the OpenCRAVAT/Bioconductor interface

The oc2bioc R package interfaces the open-cravat Python stack to R. You can use this package by pulling the vjcitn/biocopencravat docker container and running it via

# bash version
docker run -ti vjcitn/biocopencravat bash

or

# rstudio version
docker run -e PASSWORD=<choose a password> -p 8787:8787 vjcitn/biocopencravat

For the bash version, start R and then do library(oc2bioc). Only one open-cravat python module is currently exposed, cravat.admin_util.search_remote, which is called with argument (".*") in populate_module_set. Further work will expose more functionality.

For the rstudio version, point a browser to localhost:8787 and use rstudio as username, and whatever you chose for PASSWORD as password. library(oc2bioc) will succeed.

Have a look at the vignette at Get started for more details.