Welcome to BEDbase

BEDbase is a unified platform for aggregating, analyzing, and serving genomic region data. BEDbase redefines the way to manage genomic region data and allows users to search for BED files of interest and create collections tailored to research needs. BEDbase is composed of a web server and an API. Users can explore comprehensive descriptions of specific BED files via a user-oriented web interface and programmatically interact with the data via an OpenAPI-compatible API.

Or, explore an example BED fileor an example BEDset

Web server and API

The BEDbase web server and API are designed to provide a user-friendly interface for exploring and working with genomic region data. The web server allows users to search for BED files and BED sets, view detailed information about specific files, and create collections of files.

Python

Curl

JavaScript

import requests

res = requests.get(
    'https://api-dev.bedbase.org/v1/bed/example'
)

print(res.json())

library(httr)

res <- GET('https://api-dev.bedbase.org/v1/bed/example')

print(content(res, 'text'))

curl https://api-dev.bedbase.org/v1/bed/example \
    -H 'Accept: application/json' \

fetch('https://api-dev.bedbase.org/v1/bed/example')
  .then((res) => res.json())
  .then((data) => console.log(data));

Search for BED files

BEDbase offers three search endpoints for discovering BED files and BEDsets, distinguishing itself from other platforms by utilizing vector search to index and search through bed file regions. This approach enhances search accuracy and efficiency compared to platforms relying on unstructured user-provided metadata, which can be ambiguous and less reliable. User can search for BED files by providing a query string, or a BED file.

BEDbase client

BEDbase provides a Python an R client for interacting with the BEDbase API. The client allows users to download, cache, and analyze BED files and BED sets programmatically, without the need to interact with the native API. BBclient is available on PyPI in geniml package with other useful tools for genomic data analysis. Python Geniml package: PyPI geniml. R package: BEDbaser.

Python

from geniml.bbclient import BBClient

bbclient = BBClient()

regionset = bbclient.load_bed("02c7821a715f1f890ed2ae53d371072b")
print(regionset)

library(bedbaser)

api <- BEDbase()

bed_granges <- bb_to_granges(api, "02c7821a715f1f890ed2ae53d371072b")
print(bed_granges)

Data Availability Summary

Number of bed files available:0
Number of bed sets available:0
Number of genomes available:0