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svviz

Read visualizer for structural variants

https://github.com/svviz/svviz

Science Score: 23.0%

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

  • ○
    CITATION.cff file
  • ○
    codemeta.json file
  • ○
    .zenodo.json file
  • ✓
    DOI references
    Found 3 DOI reference(s) in README
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    3 of 5 committers (60.0%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (14.6%) to scientific vocabulary
Last synced: 11 months ago · JSON representation

Repository

Read visualizer for structural variants

Basic Info
  • Host: GitHub
  • Owner: svviz
  • License: mit
  • Language: Python
  • Default Branch: master
  • Homepage:
  • Size: 148 MB
Statistics
  • Stars: 84
  • Watchers: 6
  • Forks: 15
  • Open Issues: 2
  • Releases: 0
Created over 11 years ago · Last pushed almost 8 years ago
Metadata Files
Readme License

README.rst 

.. image:: https://raw.githubusercontent.com/svviz/svviz/master/docs/example.png
    :width: 80%
    :align: center

*****
svviz
*****

Author: Noah Spies

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**svviz version 2.0** is available here: `https://github.com/nspies/svviz2 `_ with `documentation here `_. For most purposes, I recommend using the new version.

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``svviz`` visualizes high-throughput sequencing data relevant to a structural variant. Only reads supporting the variant or the reference allele will be shown. svviz can operate in both an interactive web browser view to closely inspect individual variants, or in batch mode, allowing multiple variants (annotated in a VCF file) to be analyzed simultaneously.

Visit the `project site `_ for a tour of the features and example output.


.. _pypi: http://svviz.readthedocs.io/en/latest/install.html


    
Quickstart
==========

svviz has been tested on Mac OS X and Linux, and should work on Windows, although that has not been tested.

1. Ensure that you have a working compiler by following `these instructions `_ (OS X only) and that `python `_ and the python package `pip `_ are installed.
2. Install the latest version of svviz from github using the following terminal command: ``sudo pip install -U svviz``. (The sudo may not be necessary depending on your setup.)
3. Run the following command, which downloads example data and runs it through svviz: ``svviz demo``. After several processing steps, a web browser window should open, with separate, interactive views of the reference and alternate alleles.

See the `documentation `_ for more detailed help, or run ``svviz -h`` to get help on command line arguments.

Please submit bug reports or feature requests on the `github issue tracker `_.

Publication
-----------

svviz has been `published in Bioinformatics `_. If you found svviz useful for your research, please cite svviz as follows:

Spies N, Zook JM, Salit M, Sidow A. 2015. svviz: a read viewer for validating structural variants. Bioinformatics doi:bioinformatics/btv478.

Owner

  • Name: svviz
  • Login: svviz
  • Kind: organization

GitHub Events

Total
  • Watch event: 3
Last Year
  • Watch event: 3

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 321
  • Total Committers: 5
  • Avg Commits per committer: 64.2
  • Development Distribution Score (DDS): 0.044
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Noah Spies n****s@s****u 307
Noah n****s 6
Noah Spies n****s@e****l 5
apregier a****r@g****u 2
Avinash Ramu a****u@g****u 1
Committer Domains (Top 20 + Academic)
genome.wustl.edu: 2 stanford.edu: 1

Issues and Pull Requests

Last synced: 11 months ago

All Time
  • Total issues: 52
  • Total pull requests: 3
  • Average time to close issues: 2 months
  • Average time to close pull requests: about 14 hours
  • Total issue authors: 19
  • Total pull request authors: 2
  • Average comments per issue: 2.33
  • Average comments per pull request: 0.33
  • Merged pull requests: 3
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 1
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 1
  • Pull request authors: 0
  • Average comments per issue: 0.0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • nspies (27)
  • jzook (6)
  • nh13 (2)
  • sandoro (2)
  • ranasats (1)
  • zeeev (1)
  • fritzsedlazeck (1)
  • rpadmanabhan (1)
  • Karhide (1)
  • pcantalupo (1)
  • rcastil (1)
  • crazyhottommy (1)
  • z65263299 (1)
  • gatoravi (1)
  • ifiddes-10x-zz (1)
Pull Request Authors
  • apregier (2)
  • gatoravi (1)
Top Labels
Issue Labels
enhancement (14) bug (7) documentation (3) someday (3) distribution (1)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 105 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 2
  • Total versions: 21
  • Total maintainers: 1
pypi.org: svviz

A read visualizer for structural variants

  • Versions: 21
  • Dependent Packages: 0
  • Dependent Repositories: 2
  • Downloads: 105 Last month
Rankings
Stargazers count: 7.8%
Forks count: 9.1%
Dependent packages count: 10.0%
Average: 10.8%
Dependent repos count: 11.6%
Downloads: 15.6%
Maintainers (1)
nspies
Last synced: 11 months ago

Dependencies

setup.py pypi
  • flask *
  • numpy *
  • pyfaidx *
  • pysam *
  • requests *
  • six *