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wrangling-genomics

Data Wrangling and Processing for Genomics

https://github.com/datacarpentry/wrangling-genomics

Science Score: 67.0%

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    Found 7 DOI reference(s) in README
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    Links to: zenodo.org
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    Low similarity (7.3%) to scientific vocabulary

Keywords

carpentries data-carpentry data-wrangling english genomics lesson programming shell stable
Last synced: 4 months ago · JSON representation ·

Repository

Data Wrangling and Processing for Genomics

Basic Info
Statistics
  • Stars: 72
  • Watchers: 23
  • Forks: 154
  • Open Issues: 50
  • Releases: 3
Topics
carpentries data-carpentry data-wrangling english genomics lesson programming shell stable
Created almost 11 years ago · Last pushed 4 months ago
Metadata Files
Readme Contributing License Code of conduct Citation Authors Zenodo

README.md

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Wrangling Genomics

Lesson for quality control and wrangling genomics data. This repository is maintained by Josh Herr, Ming Tang, and Fotis Psomopoulos.

Amazon public AMI for this tutorial is "dataCgen-qc".

Background

Wrangling genomics trains novice learners on a variant calling workflow. Participants will learn how to evaluate sequence quality and what to do if it is not good. We will then cover aligning reads to a genome, and calling variants, as well as discussing different file formats. Results will be visualized. Finally, we will cover how to automate the process by building a shell script.

This lesson is part of the Data Carpentry Genomics Workshop.

Contribution

Code of Conduct

All participants should agree to abide by the Data Carpentry Code of Conduct.

Authors

Wrangling genomics is authored and maintained by the community.

Citation

Please cite as:

Erin Alison Becker, Taylor Reiter, Fotis Psomopoulos, Sheldon John McKay, Jessica Elizabeth Mizzi, Jason Williams, … Winni Kretzschmar. (2019, June). datacarpentry/wrangling-genomics: Data Carpentry: Genomics data wrangling and processing, June 2019 (Version v2019.06.1). Zenodo. http://doi.org/10.5281/zenodo.3260609

Owner

  • Name: Data Carpentry
  • Login: datacarpentry
  • Kind: organization
  • Email: team@carpentries.org

Workshops teaching scientists basic skills for retrieving, viewing, managing, and manipulating data in an open and reproducible way.

Citation (CITATION) 

Please cite as:

Josh Herr, Ming Tang, Lex Nederbragt, Fotis Psomopoulos (eds): "Data Carpentry: Wrangling Genomics Lesson."
Version 2017.11.0, November 2017,
http://www.datacarpentry.org/wrangling-genomics/,
doi: 10.5281/zenodo.1064254

GitHub Events

Total
  • Issues event: 3
  • Watch event: 3
  • Delete event: 5
  • Issue comment event: 5
  • Push event: 45
  • Pull request review event: 2
  • Pull request event: 4
  • Fork event: 4
  • Create event: 2
Last Year
  • Issues event: 3
  • Watch event: 3
  • Delete event: 5
  • Issue comment event: 5
  • Push event: 45
  • Pull request review event: 2
  • Pull request event: 4
  • Fork event: 4
  • Create event: 2

Issues and Pull Requests

Last synced: 4 months ago

All Time
  • Total issues: 3
  • Total pull requests: 3
  • Average time to close issues: over 4 years
  • Average time to close pull requests: 9 months
  • Total issue authors: 2
  • Total pull request authors: 3
  • Average comments per issue: 1.0
  • Average comments per pull request: 1.33
  • Merged pull requests: 3
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 1
  • Pull requests: 1
  • Average time to close issues: N/A
  • Average time to close pull requests: about 22 hours
  • Issue authors: 1
  • Pull request authors: 1
  • Average comments per issue: 0.0
  • Average comments per pull request: 2.0
  • Merged pull requests: 1
  • Bot issues: 0
  • Bot pull requests: 0
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Top Authors
Issue Authors
  • sstevens2 (2)
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  • lexnederbragt (1)
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Pull Request Authors
  • carpentries-bot (2)
  • ErinBecker (2)
  • gcroci2 (1)
  • tobyhodges (1)
  • maneesha (1)
  • Hanson19 (1)
  • asntech (1)
  • froggleston (1)
  • Parcelli (1)
  • murraycadzow (1)
  • JCSzamosi (1)
Top Labels
Issue Labels
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type: template and tools (2)

Dependencies

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