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GGPA

graph-GPA: A graphical model for prioritizing GWAS results and investigating pleiotropic architecture

https://github.com/dongjunchung/ggpa

Science Score: 23.0%

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    Found 3 DOI reference(s) in README
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    Low similarity (11.8%) to scientific vocabulary
Last synced: 11 months ago · JSON representation

Repository

graph-GPA: A graphical model for prioritizing GWAS results and investigating pleiotropic architecture

Basic Info
  • Host: GitHub
  • Owner: dongjunchung
  • Language: C++
  • Default Branch: master
  • Size: 4.81 MB
Statistics
  • Stars: 1
  • Watchers: 1
  • Forks: 1
  • Open Issues: 0
  • Releases: 0
Created almost 10 years ago · Last pushed over 6 years ago

https://github.com/dongjunchung/GGPA/blob/master/ 

[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3687182.svg)](https://doi.org/10.5281/zenodo.3687182)

graph-GPA
===

graph-GPA is a graphical model for prioritizing GWAS results and investigating pleiotropic architecture (Chung et al., 2017). 'GGPA' package provides user-friendly interface to fit graph-GPA models, implement association mapping, and generate a phenotype graph. From its version 0.9.5, it also allows to utilize a prior phenotype graph (Kim et al., 2017).

DDNet
===

DDNet is a web interface to infer the disease-disease network from the literature mining. Using DDNet, users can query diseases of interest, investigate relationship among these diseases visually and dynamically, and download various information including an adjacency matrix. This adjacency matrix can be used as a prior phenotype graph to guide the estimation of pleiotropic architecture. Please refer Kim et al. (2017) and the R package vignette for more details. DDNet is accessible from the following web address: 

http://chunglab.io/ddnet/

Installation
===========

To install the development version of GGPA, it's easiest to use the 'devtools' package. Note that GGPA depends on the 'Rcpp' package, which also requires appropriate setting of Rtools and Xcode for Windows and Mac OS/X, respectively.

```
#install.packages("devtools")
library(devtools)
install_github("dongjunchung/GGPA")
```

Usage
===========

The R package vignette will provide a good start point for the genetic analysis using GGPA package, including the overview of GGPA package and the example command lines:

```
library(GGPA)
vignette("GGPA-example")
```
The following two help pages will also provide quick references for GGPA package and the example command lines:

```
package?GGPA
class?GGPA
```

References
==========

Chung D, Kim H, and Zhao H (2017), "graph-GPA: A graphical model for prioritizing GWAS results and investigating pleiotropic architecture," *PLOS Computational Biology*, 13(2): e1005388.

Kim H, Yu Z, Lawson A, Zhao H, and Chung D (2018), "Improving SNP prioritization and pleiotropic architecture estimation by incorporating prior knowledge using graph-GPA," *Bioinformatics*, bty061.

Owner

  • Name: Dongjun Chung
  • Login: dongjunchung
  • Kind: user
  • Location: Columbus, OH
  • Company: The Ohio State University

GitHub Events

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Last synced: over 2 years ago

All Time
  • Total Commits: 22
  • Total Committers: 2
  • Avg Commits per committer: 11.0
  • Development Distribution Score (DDS): 0.091
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  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Dongjun Chung d****g@g****m 20
Dongjun Chung d****g@D****l 2

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Last synced: 11 months ago

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  • Total issues: 0
  • Total pull requests: 0
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  • Average comments per issue: 0
  • Average comments per pull request: 0
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Packages

  • Total packages: 1
  • Total downloads:
    • bioconductor 8,465 total
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 5
  • Total maintainers: 1
bioconductor.org: GGPA

graph-GPA: A graphical model for prioritizing GWAS results and investigating pleiotropic architecture

  • Versions: 5
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 8,465 Total
Rankings
Dependent repos count: 0.0%
Dependent packages count: 0.0%
Average: 26.4%
Downloads: 79.2%
Maintainers (1)
dongjun.chung@gmail.com
Last synced: 11 months ago

Dependencies

DESCRIPTION cran
  • GGally * depends
  • graphics * depends
  • methods * depends
  • Rcpp >= 0.11.3 imports