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Open Source Science

https://github.com/broadinstitute/pyqtl

Collection of analysis tools for quantitative trait loci

https://github.com/broadinstitute/pyqtl

Science Score: 36.0%

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
  • ✓
    Committers with academic emails
    1 of 2 committers (50.0%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (7.1%) to scientific vocabulary
Last synced: 10 months ago · JSON representation

Repository

Collection of analysis tools for quantitative trait loci

Basic Info
  • Host: GitHub
  • Owner: broadinstitute
  • License: bsd-3-clause
  • Language: Python
  • Default Branch: master
  • Size: 356 KB
Statistics
  • Stars: 58
  • Watchers: 5
  • Forks: 11
  • Open Issues: 2
  • Releases: 0
Created almost 7 years ago · Last pushed 11 months ago
Metadata Files
Readme License

README.md

pyQTL

pyQTL is a python module for analyzing and visualizing quantitative trait loci (QTL) data.

The following functionalities are provided: * qtl.annotation: class for working with gene annotations; includes a GTF parser. * qtl.coloc: Python implementation of core functions from the R COLOC package. * qtl.io: functions for reading/writing BED and GCT files. * qtl.locusplot: functions for generating LocusZoom-style regional association plots. * qtl.pileup: functions for visualizing QTL effects in read pileups from, e.g., RNA-seq data. * qtl.plot: plotting functions for QTLs.

Install

You can install pyQTL using pip: pip3 install qtl or directly from this repository: ``` $ git clone git@github.com:broadinstitute/pyqtl.git $ cd pyqtl

set up virtual environment and install

$ virtualenv venv $ source venv/bin/activate (venv)$ pip install -e . ```

Owner

  • Name: Broad Institute
  • Login: broadinstitute
  • Kind: organization
  • Location: Cambridge, MA

Broad Institute of MIT and Harvard

GitHub Events

Total
  • Issues event: 2
  • Watch event: 10
  • Issue comment event: 2
  • Push event: 27
  • Fork event: 3
  • Create event: 1
Last Year
  • Issues event: 2
  • Watch event: 10
  • Issue comment event: 2
  • Push event: 27
  • Fork event: 3
  • Create event: 1

Committers

Last synced: about 1 year ago

All Time
  • Total Commits: 188
  • Total Committers: 2
  • Avg Commits per committer: 94.0
  • Development Distribution Score (DDS): 0.005
Past Year
  • Commits: 32
  • Committers: 1
  • Avg Commits per committer: 32.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
francois-a f****s@b****g 187
Francois Aguet f****t@i****m 1
Committer Domains (Top 20 + Academic)
illumina.com: 1 broadinstitute.org: 1

Issues and Pull Requests

Last synced: 11 months ago

All Time
  • Total issues: 5
  • Total pull requests: 3
  • Average time to close issues: 5 days
  • Average time to close pull requests: 13 days
  • Total issue authors: 5
  • Total pull request authors: 3
  • Average comments per issue: 1.0
  • Average comments per pull request: 0.0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 3
  • Pull requests: 1
  • Average time to close issues: 8 days
  • Average time to close pull requests: 13 days
  • Issue authors: 3
  • Pull request authors: 1
  • Average comments per issue: 1.33
  • Average comments per pull request: 0.0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • majgah (1)
  • liqingbioinfo (1)
  • zhangpicb (1)
  • liaguiro (1)
  • t-silvers (1)
Pull Request Authors
  • georgettica (2)
  • ActioTom (1)
  • julianhess (1)
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 723 last-month
  • Total docker downloads: 276,318
  • Total dependent packages: 1
  • Total dependent repositories: 4
  • Total versions: 10
  • Total maintainers: 1
pypi.org: qtl

Utilities for analyzing and visualizing QTL data

  • Documentation: https://qtl.readthedocs.io/
  • License: BSD 3-Clause License Copyright (c) 2019, The Broad Institute, Inc. and The General Hospital Corporation. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
  • Latest release: 0.1.10
    published over 1 year ago
  • Versions: 10
  • Dependent Packages: 1
  • Dependent Repositories: 4
  • Downloads: 723 Last month
  • Docker Downloads: 276,318
Rankings
Docker downloads count: 0.9%
Dependent packages count: 4.7%
Average: 7.0%
Dependent repos count: 7.5%
Downloads: 15.0%
Maintainers (1)
francois-a
Last synced: 11 months ago

Dependencies

setup.py pypi
  • bx-python *
  • matplotlib *
  • numpy *
  • pandas *
  • pyBigWig *
  • scipy *
  • seaborn *