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https://github.com/databio/bedboss

Python pipeline for processing BED files for BEDbase

https://github.com/databio/bedboss

Science Score: 26.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ○
    Academic email domains
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (12.9%) to scientific vocabulary

Keywords

bed-files bed-format genomic-intervals geo
Last synced: 6 months ago · JSON representation

Repository

Python pipeline for processing BED files for BEDbase

Basic Info
  • Host: GitHub
  • Owner: databio
  • License: bsd-2-clause
  • Language: Jupyter Notebook
  • Default Branch: main
  • Homepage: https://docs.bedbase.org
  • Size: 23.1 MB
Statistics
  • Stars: 1
  • Watchers: 3
  • Forks: 0
  • Open Issues: 16
  • Releases: 14
Topics
bed-files bed-format genomic-intervals geo
Created about 3 years ago · Last pushed 6 months ago
Metadata Files
Readme License

README.md

bedboss

[![PEP compatible](https://pepkit.github.io/img/PEP-compatible-green.svg)](https://pep.databio.org/) ![Run pytests](https://github.com/bedbase/bedboss/workflows/Run%20instalation%20test/badge.svg) [![pypi-badge](https://img.shields.io/pypi/v/bedboss?color=%2334D058)](https://pypi.org/project/bedboss) [![pypi-version](https://img.shields.io/pypi/pyversions/bedboss.svg?color=%2334D058)](https://pypi.org/project/bedboss) [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black) [![Github badge](https://img.shields.io/badge/source-github-354a75?logo=github)](https://github.com/databio/bedboss)

Documentation: https://docs.bedbase.org/bedboss

Source Code: https://github.com/databio/bedboss

BEDboss is a command-line management tool for BEDbase. It contains pipelines that filters, standardizes, and calculates statistics for genomic interval data, functions that enters the results into a BEDbase database, deletes bed and bedsets from the database, and indexes the data to qdrant.

Installation

To install bedboss use this command: pip install bedboss or install the latest version from the GitHub repository: pip install git+https://github.com/databio/bedboss.git

Development

For development, you should install all the dependencies, create a virtual environment, and work on the local database. The workflow is described in the development documentation.

Testing

Requirements test:

To test requirements, install bedboss and run:

bedboss requirements-check

Smoke tests:

Use this docs: - ./test/README.md

How to generate usage documentation:

Run this command in the root of the repository: cd scripts bash update_usage_docs.sh

Owner

  • Name: Databio
  • Login: databio
  • Kind: organization
  • Location: University of Virginia

Solving problems in computational biology

GitHub Events

Total
  • Create event: 16
  • Release event: 4
  • Issues event: 52
  • Delete event: 13
  • Issue comment event: 58
  • Member event: 2
  • Push event: 185
  • Pull request review comment event: 50
  • Pull request review event: 42
  • Pull request event: 29
Last Year
  • Create event: 16
  • Release event: 4
  • Issues event: 52
  • Delete event: 13
  • Issue comment event: 58
  • Member event: 2
  • Push event: 185
  • Pull request review comment event: 50
  • Pull request review event: 42
  • Pull request event: 29

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 79
  • Total pull requests: 56
  • Average time to close issues: 4 months
  • Average time to close pull requests: 17 days
  • Total issue authors: 6
  • Total pull request authors: 4
  • Average comments per issue: 1.84
  • Average comments per pull request: 0.23
  • Merged pull requests: 52
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 32
  • Pull requests: 33
  • Average time to close issues: 3 months
  • Average time to close pull requests: 14 days
  • Issue authors: 4
  • Pull request authors: 3
  • Average comments per issue: 1.69
  • Average comments per pull request: 0.12
  • Merged pull requests: 29
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • khoroshevskyi (50)
  • donaldcampbelljr (17)
  • nsheff (10)
  • jwokaty (2)
  • sanghoonio (1)
  • xuebingjie1990 (1)
Pull Request Authors
  • khoroshevskyi (54)
  • donaldcampbelljr (14)
  • nsheff (3)
  • xuebingjie1990 (2)
Top Labels
Issue Labels
likely-solved (22) enhancement (9) bedClassifier (7) brainstorming (5) wontfix (2) question (2) dependencies (1) high-priority (1) help wanted (1) bug (1) priority-high (1) blocked (1)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 215 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 14
  • Total maintainers: 2
pypi.org: bedboss

Pipelines for genomic region file to produce bed files, and it's statistics

  • Versions: 14
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 215 Last month
Rankings
Dependent packages count: 7.6%
Forks count: 30.4%
Average: 36.7%
Stargazers count: 39.3%
Dependent repos count: 69.4%
Maintainers (2)
nsheff databio
Last synced: 6 months ago