Tag: Association Testing

pyGenClean 1.8.3 – Tool for Genetic Data Clean up before Association Testing

pyGenClean 1.8.3

:: DESCRIPTION

pyGenClean is an informatics tool to facilitate and standardize the genetic data clean up pipeline with genotyping array data. In conjuction with a source batch-queuing system, the tool minimizes data manipulation errors, it accelerates the completion of the data clean up process and it provides informative graphics and metrics to guide decision making for statistical analysis.

::DEVELOPER

Marie-Pierre Dubé’s Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /  Windows / MacOsX
  • Python

:: DOWNLOAD
 pyGenClean

:: MORE INFORMATION

Citation

Bioinformatics. 2013 May 30. [Epub ahead of print]
pyGenClean: efficient tool for genetic data clean up before association testing.
Lemieux Perreault LP, Provost S, Legault MA, Barhdadi A, Dubé MP.

gTDT 0.01 – A group-wise TDT for Haplotype-based Association Testing of Rare Variants with complex Disease

gTDT 0.01

:: DESCRIPTION

gTDT implemented gene-based or group-wise TDT for rare variant aggregation analysis. Currently gTDT implemented haplotype-based tests for 6 models, M1-M6. It takes as input a ped file and a dat file that specify the relationships, and a VCF file that stores genotype data.

::DEVELOPER

gTDT team

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux

:: DOWNLOAD

 gTDT 

:: MORE INFORMATION

Citation

A haplotype-based framework for group-wise transmission/disequilibrium tests for rare variant association analysis.
Chen R, Wei Q, Zhan X, Zhong X, Sutcliffe J, Cox N, Cook EH, Li C, Chen W, Li B.
Bioinformatics. 2015 Jan 6. pii: btu860.

aSPU 1.50 – Adaptive Gene- and Pathway-Trait Association Testing with GWAS

aSPU 1.50

:: DESCRIPTION

aSPU is an R package for adaptive sum of powered score test(ASPU) in genetic association studies.

::DEVELOPER

Il-Youp Kwak

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /  MacOsX / Window
  • R

:: DOWNLOAD

 aSPU

:: MORE INFORMATION

Citation

Adaptive Gene- and Pathway-Trait Association Testing with GWAS Summary Statistics.
Kwak IY, Pan W.
Bioinformatics. 2015 Dec 10. pii: btv719.

UNCcombo 0.1 – Likelihood based Association Testing for NGS data without intermediate Genotype Galling

UNCcombo 0.1

:: DESCRIPTION

UNCcombo is a R package to perform single marker association testing on raw next generation sequencing data.

::DEVELOPER

Yun Li Statistical Genetics Group

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux/ MacOsX
  • R

:: DOWNLOAD

 UNCcombo

:: MORE INFORMATION

Citation

Likelihood Based Complex Trait Association Testing for Arbitrary Depth Sequencing Data.
Yan S, Yuan S, Xu Z, Zhang B, Zhang B, Kang G, Byrnes A, Li Y.
Bioinformatics. 2015 May 14. pii: btv307.

GraphIBD 0.1.0 – Fast IBD Association Testing given Genome-wide SNP data

GraphIBD 0.1.0

:: DESCRIPTION

GraphIBD is a free, open-source IBD association testing software for genome-wide association study analysis. GraphIBD requires an IBD detection method such as Beagle FastIBD to run first. Then GraphIBD builds upon the IBD information to test if the IBD segments show association to the traits.

::DEVELOPER

Buhm Han

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX/Windows
  • Java

:: DOWNLOAD

 GraphIBD

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Dec 13.
Fast pairwise IBD association testing in genome-wide association studies.
Han B, Kang EY, Raychaudhuri S, de Bakker PI, Eskin E.

LIBFBAT 0.5.1 – C++ library for Family Based Association Testing

LIBFBAT 0.5.1

:: DESCRIPTION

LIBFBAT programming library s robust both to genotyping errors and missing genotypes. The underlying method consists in considering an incomplete data model where the true unobserved genotypes produce the observed one through an explicit genotyping error model.

::DEVELOPER

LIBFBAT team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Mac OsX/ Linux
  • C++ Compiler

:: DOWNLOAD

LIBFBAT

:: MORE INFORMATION

Citation

Gregory Nuel, Yousri Slaoui and Vincent Miele,
libfbat: a C++ library for family based association testing,
Proceedings of JOBIM, 2008

PODKAT 1.18.0 – Association Testing Involving Rare and Private Variants

PODKAT 1.18.0

:: DESCRIPTION

The podkat package provides an association test that is capable of dealing with very rare and even private variants. This is accomplished by a kernel-based approach that takes the positions of the variants into account. The test can be used for pre-processed matrix data, but also directly for variant data stored in VCF files. Association testing can be performed whole-genome, whole-exome, or restricted to pre-defined regions of interest. The test is complemented by tools for analyzing and visualizing the results.

::DEVELOPER

Institute of Bioinformatics, Johannes Kepler University Linz

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux / MacOsX
  • R
  • BioConductor

:: DOWNLOAD

PODKAT

:: MORE INFORMATION

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