KBAS 1.0 – Knowledge-Based Association Study

KBAS 1.0

:: DESCRIPTION

KBAS is a software package to perform genome-wide association studies in situations in which combinations of SNPs jointly contribute to the traits of interest, as is often the case in complex diseases with a genetic basis.

::DEVELOPER

University of Florida Genetics Institute

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 KBAS

:: MORE INFORMATION

Citation

A knowledge-based method for association studies on complex diseases.
Nazarian A, Sichtig H, Riva A.
PLoS One. 2012;7(9):e44162.

ESPRESSO 1.0 – Account Assessment Errors on Outcome and Exposures in Power Analysis for Association Studies

ESPRESSO 1.0

:: DESCRIPTION

ESPRESSO (Estimating Sample-size and Power in R by Exploring Simulated Study Outcomes) is a simulation based tool, written in the R language that supports power and sample size calculations for stand-alone studies and analyses nested in cohort studies. The large number of participants required for adequately powered studies are quite expensive so it is important that an accurate sample size is identified.

::DEVELOPER

ESPRESSO team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /  Windows
  • R

:: DOWNLOAD

 ESPRESSO

:: MORE INFORMATION

Citation:

ESPRESSO: taking into account assessment errors on outcome and exposures in power analysis for association studies.
Gaye A, Burton TW, Burton PR.
Bioinformatics. 2015 Apr 22. pii: btv219.

WISARD – Workbench for Integrated Superfast Association study with Related Data

WISARD 1.1.0.9

:: DESCRIPTION

WISARD is a free and comprehensive Statistical Analysis toolkit for omics data.

::DEVELOPER

WISARD team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / Mac OsX

:: DOWNLOAD

 WISARD

:: MORE INFORMATION

Citation

Lee S, Choi S, Yoon J, Park T and Won S,
“A workbench for family-based genetic analysis using next-generation DNA sequencing data”,
submitted.

SPOT – Biological Prioritization after a SNP Association Study

SPOT

:: DESCRIPTION

SPOT (SNP Prioritization Online Tool) is a web‐based program that prioritizes the results of a genetic association study using genomic annotation data.Given a collection that are to receive higher priority when selecting SNPs for further study after an initial genetic association study, SPOT offers a systematic way of doing this while taking into a account a variety range of additional biological information.

::DEVELOPER

SPOT team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2010 Jul;38(Web Server issue):W201-9. doi: 10.1093/nar/gkq513. Epub 2010 Jun 6.
SPOT: a web-based tool for using biological databases to prioritize SNPs after a genome-wide association study.
Saccone SF1, Bolze R, Thomas P, Quan J, Mehta G, Deelman E, Tischfield JA, Rice JP.

CLUMP 2.4 – Assess Significance of Case-control Association Studies with Multi-allelic Markers

CLUMP 2.4

:: DESCRIPTION

CLUMP is a program designed to assess the significance of the departure of observed values in a contingency table from the expected values conditional on the marginal totals. The present implementation works on 2 x N tables and was designed for use in genetic case-control association studies, but the program should be useful for any 2 x N contingency table, especially where N is large and the table is sparse. The significance is assessed using a Monte Carlo approach, by performing repeated simulations to generate tables having the same marginal totals as the one under consideration, and counting the number of times that a chi-squared value associated with the real table is achieved bythe randomly simulated data. This means that the significance levels assigned should be unbiased (with accuracy dependent on the number of simulations performed) and that no special account needs to be taken of continuity corrections or small expected values.

::DEVELOPER

Dave Curtis

:: SCREENSHOTS

Command Line

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

CLUMP

:: MORE INFORMATION

Citation:

Sham PC & Curtis D. 1995.
Monte Carlo tests for associations between disease and alleles at highly polymorphic loci.
Ann Hum Genet. 59: 97-105.

POWERDESIGN – Association Study Design Server

POWERDESIGN

:: DESCRIPTION

POWERDESIGN selects tag SNPs to maximize power.Association study design server efficiently designs a study to maximize statistical power given a genetic region of interest, by quickly aproximating the power of each candidate design.

::DEVELOPER

Buhm Han

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Ann Hum Genet. 2008 Nov;72(Pt 6):834-47. doi: 10.1111/j.1469-1809.2008.00469.x. Epub 2008 Aug 13.
Efficient association study design via power-optimized tag SNP selection.
Han B, Kang HM, Seo MS, Zaitlen N, Eskin E.

PIAGE 1.0 – Power of Indirect Association Studies of Gene-Environment Interactions

PIAGE 1.0

:: DESCRIPTION

PIAGE (Power of Indirect Association Studies of Gene-Environment Interactions) performs estimation of power and sample sizes required to detect genetic and environmental main, as well as gene-environment interaction (GxE) effects in indirect matched case-control studies (1:1 matching). When the hypothesis of GxE is tested, power/sample size will be estimated for the detection of GxE, as well as for the detection of genetic and environmental marginal effects. Furthermore, power estimation is implemented for the joint test of genetic marginal and GxE effects

::DEVELOPER

Division of Cancer Epidemiology, German Cancer Research Center

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

  PIAGE

:: MORE INFORMATION

Citation

Genet Epidemiol. 2008 Apr;32(3):235-45.
Sample size requirements for indirect association studies of gene-environment interactions (G x E).
Hein R, Beckmann L, Chang-Claude J.

SPREG 2.0 – Regression Analysis of Secondary Phenotype Data in Case-Control Association Studies

SPREG 2.0

:: DESCRIPTION

SPREG is a computer program for performing regression analysis of secondary phenotype data in case-control association studies. Secondary phenotypes are quantitative or qualitative traits other than the case-control status. Because the case-control sample is not a random sample of the general population, standard statistical analysis of secondary phenotype data can yield very misleading results.

::DEVELOPER

Danyu Lin

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux

:: DOWNLOAD

 SPREG

:: MORE INFORMATION

Citation

Lin DY, Zeng D. 2009,
Proper analysis of secondary phenotype data in case-control association studies,
Genetic Epidemiology, 33:256-265.

gs 2.0 – Generating Samples for Association Studies based on HapMap data

gs 2.0

:: DESCRIPTION

gs can be used to generate samples in testing algorithms for tag SNP selection, haplotype inference, as well as epistatic detection.

::DEVELOPER

Jing Li

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux /MacOsX

:: DOWNLOAD

 gs

:: MORE INFORMATION

Citation

Li, J and Y Chen.
Generating samples for association studies based on HapMap data.
BMC Bioinformatics 9:44, 2008.