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genomedata

The Genomedata format for storing large-scale functional genomics data.

https://github.com/hoffmangroup/genomedata

Science Score: 44.0%

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    Low similarity (11.6%) to scientific vocabulary
Last synced: 6 months ago · JSON representation ·

Repository

The Genomedata format for storing large-scale functional genomics data.

Basic Info
Statistics
  • Stars: 2
  • Watchers: 2
  • Forks: 1
  • Open Issues: 42
  • Releases: 6
Created almost 6 years ago · Last pushed 6 months ago
Metadata Files
Readme Changelog Contributing License Citation

README.rst 

============
 Genomedata
============
by Michael Hoffman 

.. image:: https://img.shields.io/pypi/v/genomedata.png
    :target: https://pypi.python.org/pypi/genomedata/
    :alt: Latest Version

Description
===========
Genomedata is both a format for efficient storage of multiple tracks of
numeric data anchored to a genome and a python interface to genomic datasets.
The file format allows fast random access to hundreds of gigabytes of data, 
while retaining a small disk space footprint. We have also developed utilities
to load data into this format.

Specifically, the genomedata package provides access to genome-scale data,
either using an HDF5_ container or a bigWig_ file.

.. _HDF5: http://www.hdfgroup.org/
.. _bigWig: http://www.genome.ucsc.edu/goldenPath/help/bigWig.html

Please see the following URL (and linked documentation) for information,
installation, and support: https://hoffmanlab.org/proj/genomedata/

Documentation
=============

Live documentation based on this repository can be found on `Read the Docs`_.

.. _Read the Docs: http://genomedata.readthedocs.io/en/latest/

License
========
Genomedata is free software: you can redistribute it and/or modify it under the terms of version 2 of the GNU General Public License as published by the Free Software Foundation.

Genomedata is distributed in the hope that it will be useful, but WITHOUT
ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
FITNESS FOR A PARTICULAR PURPOSE.

Owner

  • Name: hoffmangroup
  • Login: hoffmangroup
  • Kind: organization

Citation (CITATION.cff) 

cff-version: 1.2.0
title: Genomedata
version: 1.5.0
date-released: "2020-01-08"
message: If you use this software, please cite both the article from preferred-citation and the software itself.
abstract: This software implements a method of fast random access of numeric data anchored to a genome
authors:
  - family-names: Hoffman
    given-names: Michael M.
    affiliation: "University Health Network"
    orcid: "https://orcid.org/0000-0002-4517-1562"
license: GPL-2.0-only
repository-code: "https://github.com/hoffmangroup/genomedata"
url: "https://genomedata.hoffmanlab.org"
preferred-citation:
  type: edited-work
  title: The Genomedata format for storing large-scale functional genomics data
  year: 2010
  authors:
    - family-names: Hoffman
      given-names: Michael M.
      affiliation: "University of Washington"
      orcid: "https://orcid.org/0000-0002-4517-1562"
    - family-names: Buske
      given-names: Orion J.
      affiliation: "University of Washington"
      orcid: "https://orcid.org/0000-0002-9064-092X"
    - family-names: Bilmes
      given-names: Jeff A.
      affiliation: "University of Washington"
      orcid: "https://orcid.org/0000-0002-7372-8778"
    - family-names: Noble
      affiliation: "University of Washington"
      orcid: "https://orcid.org/0000-0001-7283-4715"
      given-names: William Stafford
  doi: doi.org/10.1093/bioinformatics/btq164
  volume: 26
  issue: 11
  journal: "Bioinformatics"
  publisher:
    name: "Oxford University Press"

GitHub Events

Total
  • Push event: 5
  • Create event: 1
Last Year
  • Push event: 5
  • Create event: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 59
  • Total pull requests: 16
  • Average time to close issues: 10 months
  • Average time to close pull requests: about 2 months
  • Total issue authors: 3
  • Total pull request authors: 1
  • Average comments per issue: 2.59
  • Average comments per pull request: 0.88
  • Merged pull requests: 15
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 1
  • Average time to close issues: N/A
  • Average time to close pull requests: 2 days
  • Issue authors: 0
  • Pull request authors: 1
  • Average comments per issue: 0
  • Average comments per pull request: 1.0
  • Merged pull requests: 1
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • EricR86 (57)
  • BradBalderson (1)
  • annamalkowska (1)
Pull Request Authors
  • EricR86 (16)
Top Labels
Issue Labels
minor (31) bug (29) enhancement (26) trivial (13) major (10) critical (1) proposal (1)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 83 last-month
  • Total dependent packages: 1
  • Total dependent repositories: 4
  • Total versions: 27
  • Total maintainers: 2
pypi.org: genomedata

tools for accessing large amounts of genomic data

  • Versions: 27
  • Dependent Packages: 1
  • Dependent Repositories: 4
  • Downloads: 83 Last month
Rankings
Dependent packages count: 4.8%
Dependent repos count: 7.5%
Average: 9.1%
Downloads: 15.0%
Maintainers (2)
hoffman Eric.Roberts
Last synced: 6 months ago

Dependencies

setup.py pypi
  • numpy *
  • textinput >=0.2.0
.github/workflows/continuous-integration-workflow.yml actions
  • actions/checkout v3 composite
  • actions/setup-python v4 composite
  • actions/upload-artifact v3 composite
.github/workflows/python-publish.yml actions
  • actions/checkout v3 composite
  • actions/setup-python v4 composite
Docker/Dockerfile docker
  • ubuntu latest build
environment.yml conda
  • bedtools
  • hdf5
  • path.py
  • pytables >=3.4.3
  • python 3.8.*
  • six
  • textinput
  • ucsc-bigwigtobedgraph
  • zlib
pyproject.toml pypi
  • numpy *
  • path.py >=11
  • pybigwig *
  • six *
  • tables >=3.0,!=3.4.1
  • textinput >=0.2.0