README.md

In cellbaseR: Querying annotation data from the high performance Cellbase web

Overview

This R package makes use of the exhaustive RESTful Web service API that has been implemented for the Cellabase database. It enable researchers to query and obtain a wealth of biological information from a single database saving a lot of time. Another benefit is that researchers can easily make queries about different biological topics and link all this information together as all information is integrated.

Currently Homo sapiens, Mus musculus and a total of 48 species are available and many others will be included soon. Results returned from the cellbase queries are parsed into R data.frames and other common R data strctures so users can readily get into downstream anaysis. NB. Due to some maintance and updares on the Cellbase Server some functionality is not working, more specifically all the variants and snp annotations are not working, this will be resolved shortly.

Documentation

You can find CellBase documentation and tutorials at: https://github.com/opencb/cellbase/wiki.

For documenting RESTful web services Swagger has been set-up and is available at http://bioinfo.hpc.cam.ac.uk/cellbase/webservices/.

Issues Tracking

You can report bugs or request new features at GitHub issue tracking.

Release Notes and Roadmap

Releases notes are available at GitHub releases.

Roadmap is available at GitHub milestones. You can report bugs or request new features at GitHub issue tracking.

Maintainers

We recommend to contact CellBase developers by writing to OpenCB mailing list [e-mail]. The main developers and maintainers are: Ignacio Medina ([e-mail]) (Founder and Project Leader) Javier Lopez ([e-mail]) * Mohammed OE ([e-mail])

cellbaseR documentation built on Nov. 8, 2020, 5:38 p.m.