plinkqc

R package for quality control of plink genetic datasets

https://github.com/meyer-lab-cshl/plinkqc

Science Score: 49.0%

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
Found .zenodo.json file
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DOI references
Found 3 DOI reference(s) in README
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Academic publication links
Links to: zenodo.org
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Scientific vocabulary similarity
Low similarity (16.9%) to scientific vocabulary

Last synced: 7 months ago · JSON representation

Repository

R package for quality control of plink genetic datasets

Basic Info

Host: GitHub
Owner: meyer-lab-cshl
License: other
Language: R
Default Branch: master
Size: 21.5 MB

Statistics

Stars: 59
Watchers: 4
Forks: 27
Open Issues: 11
Releases: 9

Created over 7 years ago · Last pushed 7 months ago

Metadata Files

Readme Changelog License Code of conduct Codemeta

README.Rmd

---
output: github_document
---



```{r, echo = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "README-"
)
```

[![CRAN_Status_Badge](http://www.r-pkg.org/badges/version/plinkQC)](https://cran.r-project.org/package=plinkQC)
[![Build Status](https://travis-ci.org/meyer-lab-cshl/plinkQC.svg?branch=master)](https://travis-ci.org/meyer-lab-cshl/plinkQC)
[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
[![Downloads](http://cranlogs.r-pkg.org/badges/grand-total/plinkQC?color=blue)](https://cran.r-project.org/package=plinkQC)

##  plinkQC

**plinkQC** is a R/CRAN package for **genotype quality control** in genetic
association studies. It makes PLINK basic statistics (e.g.missing genotyping
rates per individual, allele frequencies per genetic marker) and relationship
functions easily accessible from within R and allows for automatic evaluation
of the results.


Full documentation is available at https://meyer-lab-cshl.github.io/plinkQC/.


**plinkQC** generates a per-individual and per-marker quality control report.
A step-by-step guide on how to run these analyses can be found
[here](https://meyer-lab-cshl.github.io/plinkQC/articles/plinkQC.html).

Individuals and markers that fail the quality control can subsequently be
removed with **plinkQC** to generate a new, clean dataset.

**plinkQC** facilitates an ancestry check for study individuals based on
comparison to reference datasets. The processing of the reference datasets is
documented in detail
[here](https://meyer-lab-cshl.github.io/plinkQC/articles/AncestryCheck.html).

Removal of individuals based on relationship status via **plinkQC** is optimised
to retain as many individuals as possible in the study.

##  Installation

The current github version of **plinkQC**  is: 0.3.4 and can be
installed via
```{r github install, eval=FALSE}
library(devtools)
install_github("meyer-lab-cshl/plinkQC")
```
The current CRAN version of **plinkQC**  is: 0.3.4 and can be
installed via
```{r  install, eval=FALSE}
install.packages("plinkQC")
```

A log of version changes can be found [here](https://meyer-lab-cshl.github.io/plinkQC/news/index.html).

##  Citation
Meyer HV (2020) plinkQC: Genotype quality control in genetic association
studies. [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3934294.svg)](https://doi.org/10.5281/zenodo.3934294)

Owner

Name: Meyer Laboratory
Login: meyer-lab-cshl
Kind: organization
Email: hmeyer@cshl.edu

Website: https://meyer-lab-cshl.github.io/
Repositories: 7
Profile: https://github.com/meyer-lab-cshl

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GitHub Events

Total

Issues event: 3
Watch event: 4
Issue comment event: 2
Push event: 8

Last Year

Issues event: 3
Watch event: 4
Issue comment event: 2
Push event: 8

Committers

Last synced: over 2 years ago

All Time

Total Commits: 369
Total Committers: 5
Avg Commits per committer: 73.8
Development Distribution Score (DDS): 0.187

Past Year

Commits: 0
Committers: 0
Avg Commits per committer: 0.0
Development Distribution Score (DDS): 0.0

Top Committers

Name	Email	Commits
HannahVMeyer	h**r@g**m	300
HannahVMeyer	H**r@g**m	30
Hannah	h**r@g**m	19
HannahVMeyer	H****r	19
Elika Garg	e****r	1

Issues and Pull Requests

Last synced: 8 months ago

All Time

Total issues: 45
Total pull requests: 12
Average time to close issues: about 2 months
Average time to close pull requests: about 2 hours
Total issue authors: 31
Total pull request authors: 2
Average comments per issue: 4.58
Average comments per pull request: 0.08
Merged pull requests: 12
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 3
Pull requests: 0
Average time to close issues: N/A
Average time to close pull requests: N/A
Issue authors: 2
Pull request authors: 0
Average comments per issue: 0.33
Average comments per pull request: 0
Merged pull requests: 0
Bot issues: 0
Bot pull requests: 0

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Top Authors

Issue Authors

blueskypie (6)
rskl92 (3)
HannahVMeyer (3)
montenegrina (2)
fastforward35 (2)
evagradovich (2)
fransbudiman (2)
MichaelCummingsBCH (2)
carolinewalter5 (1)
umasaxena (1)
pwuUCL (1)
nickorr78 (1)
dietmarfdz (1)
pasiunaite (1)
GabrieleNocchi (1)

Pull Request Authors

HannahVMeyer (11)
eg-r (1)

Top Labels

Issue Labels

enhancement (3) help wanted (2) bug (2) question (1) invalid (1)

Pull Request Labels

Packages

Total packages: 1
Total downloads:
- cran 436 last-month
Total docker downloads: 1,438

Total dependent packages: 0
Total dependent repositories: 0
Total versions: 10
Total maintainers: 1

cran.r-project.org: plinkQC

Genotype Quality Control with 'PLINK'

Homepage: https://meyer-lab-cshl.github.io/plinkQC/
Documentation: http://cran.r-project.org/web/packages/plinkQC/plinkQC.pdf
License: MIT + file LICENSE
Latest release: 0.3.4
published over 4 years ago

Versions: 10
Dependent Packages: 0
Dependent Repositories: 0
Downloads: 436 Last month
Docker Downloads: 1,438

Rankings

Forks count: 3.3%

Stargazers count: 8.0%

Average: 20.8%

Downloads: 27.6%

Dependent packages count: 29.8%

Dependent repos count: 35.5%

Maintainers (1)

hannah.v.meyer@gmail.com

Last synced: 7 months ago

Dependencies

DESCRIPTION cran

R >= 3.6.0 depends
R.utils * imports
UpSetR * imports
cowplot * imports
data.table >= 1.11.0 imports
dplyr * imports
ggforce * imports
ggplot2 * imports
ggrepel * imports
igraph >= 1.2.4 imports
methods * imports
optparse * imports
sys * imports
formatR * suggests
knitr * suggests
mockery * suggests
rmarkdown * suggests
testthat * suggests

ecosyste.ms

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plinkqc

Science Score: 49.0%

Repository

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Metadata Files

README.Rmd

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CodeMeta (codemeta.json)

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