Tag: Genetic Association Analysis

SUGEN v8.1 – Genetic Association Analysis Under Complex Survey Sampling

SUGEN v8.1

:: DESCRIPTION

SUGEN is a command-line software program written in C++ to implement the weighted and unweighted approaches for various types of association analysis under complex survey sampling.

::DEVELOPER

Danyu Lin

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux

:: DOWNLOAD

SUGEN

:: MORE INFORMATION

Citation

Lin DY, Tao R, Kalsbeek WD, Zeng D, Gonzalez F 2nd, Fernández-Rhodes L, Graff M, Koch GG, North KE, Heiss G.
Genetic association analysis under complex survey sampling: the Hispanic Community Health Study/Study of Latinos.
Am J Hum Genet. 2014 Dec 4;95(6):675-88. doi: 10.1016/j.ajhg.2014.11.005. PMID: 25480034; PMCID: PMC4259979.

Path 1.1.0 / Path2 0.8 – Pathway-based / Ontology , Genetic Association Analysis

Path 1.1.0 / Path2 0.8

:: DESCRIPTION

Path is designed to help researchers interface bioinformatic information from several online resources with data from genetic association studies. Path is a valuable tool for investigating gene-gene interactions in large genetic association studies. In addition, Path can be used to help store and visualize data from genetic association studies. Path is compatible with LINKAGE pre-makeped data files that are accompanied by standard QTDT data files.

Path2 is designed to conduct pathway-based analyses of Genome-wide association studies (GWASs). Path2 aims to better understand the complex nature of genetic susceptibility to complex diseases by applying pathway-based models using bioinformatics techniques.

::DEVELOPER

Genapha

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux/windows with cygwin/MacOsX
  • Java
  • Perl

:: DOWNLOAD

 Path , Path2

:: MORE INFORMATION

Citation

Zamer, Tripp, Ellis, Daley (2009),
“Path: a tool to facilitate pathway-based genetic association analysis“,
Bioinformatics, 25(18):2444-2446.

PGA – Power for Genetic Association Analysis

PGA

:: DESCRIPTION

PGA (Power for Genetic Association Analyses)is a package of algorithms and graphical user interfaces developed in Matlab for power and sample size calculation under various genetic models and statistical constraints. The software is designed to facilitate decision making for case-control association studies of candidate genes, fine-mapping studies, and whole-genome scans.

::DEVELOPER

 DCEG

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 PGA

:: MORE INFORMATION

Citation

Menashe I., Rosenberg P.S., and Chen B.E. (2008)
PGA: Power calculator for case-control genetic association analyses.
BMC Genetics, 9:36.