# BEDbase

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<img align="center" src="../img/bedbase_logo.svg" class="img-header" height="100">
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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.

## 🛰️ Services

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**Deployed public instance**: [https://bedbase.org/](https://bedbase.org/)

**API**: [https://api.bedbase.org/](https://api.bedbase.org/)

**API dev**: [https://api-dev.bedbase.org/](https://dev.bedbase.org/)

**UI**: [https://bedbase.org/](https://bedbase.org/)

**UI dev**: [https://dev.bedhost.pages.dev/](https://dev.bedhost.pages.dev/)

**Source Code**: [https://github.com/databio/bedhost/](https://github.com/databio/bedhost/)

**Object store, production** <https://data2.bedbase.org/> - base URL for cloudflare/backblaze

## 🗃️ Components

- [bedboss](https://github.com/databio/bedboss): Main BEDbase processing pipeline and managing tool, combining bedmaker, bedstat, bedbuncher, and other pipelines
- [bbconf](http://github.com/databio/bbconf): BEDbase configuration package (core of the BEDbase stack)
- [bedhost](http://github.com/databio/bedhost): FastAPI application with API for accessing data
- [bedhost-ui](http://github.com/databio/bedhost): Front-end user interface built with React
- `all_geo_beds`: A subfolder containing scripts to download all bed files on GEO using geofetch and build a backend to host the metadata using bedstat
- [geniml](https://github.com/databio/geniml): Machine learning for genomic intervals