BEDbase is a unifying platform for aggregating, analyzing and serving genomic region data as BED files. Input files are processed by a series of Python pipelines. The output of these pipelines is displayed through a RESTful API where users can access BED files along with useful statistics and plots. A project to aggregate, analyze, and serve genomic regions better (aka BED files).
Services
Deployed public instance: https://bedbase.org/
Documentation: https://docs.bedbase.org/bedhost
API dev: https://api-dev.bedbase.org/
UI dev: https://dev.bedhost.pages.dev/
Source Code: https://github.com/databio/bedhost/
Object store, production https://data2.bedbase.org/ - base URL for cloudflare/backblaze
Tutorial
There's a tutorial for bedbase in the docs_jupyter folder (probably outdated).
Components
- bedboss: Main BEDbase processing pipeline and managing tool, combining bedqc, bedmaker, bedstat, and bedbuncher
- bbconf: BEDbase configuration package (core of the BEDbase stack)
- bedhost: FastAPI application with API for accessing data
- bedhost-ui: Front-end user interface built with React
- bedbase.org repository: Repository for deploying the bedhost container to AWS.
- all_geo_beds: A subfolder, is the scripts to download all bed files on GEO using geofetch and build a backend to host the metadata using bedstat
- geniml: Machine learning for genomic intervals