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nsheff authored Dec 19, 2023
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A project to aggregate, analyze, and serve genomic regions better (*aka* BED files).

## Tutorial

There's a tutorial for bedbase in the [docs_jupyter](/docs_jupyter) folder.


## Components

- ~~[bedqc](https://github.com/databio/bedqc): a pipeline for QC of BED files.~~ moved to bedboss
- ~~[bedmaker](http://github.com/databio/bedmaker): a pipeline to convert non-bed files into bed files~~ moved to bedboss
- ~~[bedstat](http://github.com/databio/bedstat): a pipeline to calculate stats for a bed file~~ moved to bedboss
- ~~[bedbuncher](http://github.com/databio/bedbuncher): a pipeline to create bedsets~~ moved to bedboss
- ~~[bedembed](https://github.com/databio/bedembed): a pipeline to create bed file embeddings~~ now part of geniml
- [bedboss](https://github.com/databio/bedboss): main bedbase processing pipeline, combining bedqc, bedmaker, bedstat, and bedbuncher
- [bbconf](http://github.com/databio/bbconf): bedbase configuration
- [bedhost](http://github.com/databio/bedhost): FastAPI application with API for accessing data
- [bedhost-ui](http://github.com/databio/bedhost-ui): front-end user interface built with React
- [bedbase.org repository](https://github.com/databio/bedbase.org): Repository for deploying the bedhost container to AWS.
- [all_geo_beds](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

Not part of bedbase, but used by it:

- [geniml](https://github.com/databio/geniml):

## Services

- API, production: https://api.bedbase.org/
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- Front-end, dev: https://dev.bedbase.org
- Object store, production: https://data2.bedbase.org/ - base URL for cloudflare/backblaze

## Tutorial

There's a tutorial for bedbase in the [docs_jupyter](/docs_jupyter) folder (probably outdated).

## Components

- [bedboss](https://github.com/databio/bedboss): Main BEDbase processing pipeline, combining bedqc, bedmaker, bedstat, and bedbuncher
- [bbconf](http://github.com/databio/bbconf): BEDbase configuration
- [bedhost](http://github.com/databio/bedhost): FastAPI application with API for accessing data
- [bedhost-ui](http://github.com/databio/bedhost-ui): Front-end user interface built with React
- [bedbase.org repository](https://github.com/databio/bedbase.org): Repository for deploying the bedhost container to AWS.
- [all_geo_beds](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](https://github.com/databio/geniml): Machine learning for genomic intervals

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