qqman
An R package for creating Q-Q and manhattan plots from GWAS results
Science Score: 46.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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✓codemeta.json file
Found codemeta.json file -
○.zenodo.json file
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✓DOI references
Found 6 DOI reference(s) in README -
✓Academic publication links
Links to: biorxiv.org, joss.theoj.org -
✓Committers with academic emails
1 of 7 committers (14.3%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (12.4%) to scientific vocabulary
Keywords
Repository
An R package for creating Q-Q and manhattan plots from GWAS results
Basic Info
- Host: GitHub
- Owner: stephenturner
- License: gpl-3.0
- Language: HTML
- Default Branch: master
- Homepage: http://cran.r-project.org/web/packages/qqman/
- Size: 17.5 MB
Statistics
- Stars: 169
- Watchers: 15
- Forks: 92
- Open Issues: 6
- Releases: 7
Topics
Metadata Files
README.md
qqman: An R package for creating Q-Q and manhattan plots from GWAS results.
Citation
If you'd like to cite qqman (appreciated but not required), please cite the publication below:
Turner, (2018). qqman: an R package for visualizing GWAS results using Q-Q and manhattan plots. Journal of Open Source Software, 3(25), 731, https://doi.org/10.21105/joss.00731
More details are found in the preprint:
Turner, S.D. qqman: an R package for visualizing GWAS results using Q-Q and manhattan plots. biorXiv DOI: 10.1101/005165.
Installation
Install the stable release from CRAN:
r
install.packages("qqman")
Or install directly from github using devtools
r
library(devtools)
install_github("stephenturner/qqman")
Or install the most recent development release with devtools (note, there be dragons here):
r
library(devtools)
install_github("stephenturner/qqman", ref="dev")
Load the package each time you use it:
r
library(qqman)
Usage
See the online package vignette for more examples:
r
browseVignettes("qqman")
Take a look at the built-in data:
r
head(gwasResults)
Basic manhattan plot using built-in data:
r
manhattan(gwasResults)
Basic Q-Q plot using built-in data:
r
qq(gwasResults$P)
Get help:
r
?manhattan
?qq
Notes
- This release is substantially simplified for the sake of maintainability and creating an R package. The old code that allows confidence intervals on the Q-Q plot and allows more flexible annotation and highlighting is still available at the version 0.0.0 tag.
- Special thanks to Dan Capurso and Tim Knutsen for useful contributions and bugfixes.
- Thanks to all the blog commenters for pointing out bugs and other issues.
Owner
- Name: Stephen Turner
- Login: stephenturner
- Kind: user
- Location: Charlottesville, VA
- Company: @colossal-compsci
- Website: http://StephenTurner.us
- Twitter: strnr
- Repositories: 125
- Profile: https://github.com/stephenturner
Data scientist in biotech, former academic, Principal Scientist and Head of Genomic Strategy at Colossal Biosciences
GitHub Events
Total
- Issues event: 1
- Watch event: 15
- Issue comment event: 1
- Fork event: 1
Last Year
- Issues event: 1
- Watch event: 15
- Issue comment event: 1
- Fork event: 1
Committers
Last synced: 9 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| Stephen Turner | v****n@g****m | 77 |
| dcapurso | d****1@g****m | 9 |
| Xikun Han | 1****6@q****m | 3 |
| Tim Knutsen | t****n@g****m | 2 |
| Dylan Aïssi | b****n@g****m | 2 |
| hq | q****7@b****u | 1 |
| Timothée Flutre | t****e@i****r | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 60
- Total pull requests: 14
- Average time to close issues: 5 months
- Average time to close pull requests: 4 days
- Total issue authors: 51
- Total pull request authors: 11
- Average comments per issue: 2.55
- Average comments per pull request: 0.86
- Merged pull requests: 7
- 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
Top Authors
Issue Authors
- stephenturner (6)
- mcoignet (3)
- edwardphineas (2)
- tushardave26 (2)
- isp2 (1)
- renaschweizer (1)
- manuramon (1)
- zjuwhw (1)
- ParsaAkbari (1)
- NikoLichi (1)
- evad80 (1)
- kippakers (1)
- swvanderlaan (1)
- Afreen89 (1)
- neginmb (1)
Pull Request Authors
- dcapurso (3)
- timknut (2)
- samuelejones (1)
- cth (1)
- smasongarrison (1)
- daissi (1)
- GeneticResources (1)
- calpan (1)
- Liubuntu (1)
- bartosz-kozak (1)
- timflutre (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 2
-
Total downloads:
- cran 4,993 last-month
- Total docker downloads: 48,209
-
Total dependent packages: 9
(may contain duplicates) -
Total dependent repositories: 13
(may contain duplicates) - Total versions: 13
- Total maintainers: 1
proxy.golang.org: github.com/stephenturner/qqman
- Documentation: https://pkg.go.dev/github.com/stephenturner/qqman#section-documentation
- License: gpl-3.0
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Latest release: v0.1.6
published almost 8 years ago
Rankings
cran.r-project.org: qqman
Q-Q and Manhattan Plots for GWAS Data
- Homepage: https://github.com/stephenturner/qqman
- Documentation: http://cran.r-project.org/web/packages/qqman/qqman.pdf
- License: GPL-3
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Latest release: 0.1.9
published over 2 years ago
Rankings
Maintainers (1)
Dependencies
- R >= 3.0.0 depends
- calibrate * imports
- knitr * suggests
- rmarkdown * suggests