Tag: Association Analysis

Scout beta-0.9.6 – Association Analysis of Triads and Unrelated Subjects

Scout beta-0.9.6

:: DESCRIPTION

Scout is a software program for conducting combined association analysis of triads and unrelated subjects.

::DEVELOPER

Epstein software

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 Scout

:: MORE INFORMATION

Citation

Epstein MP, Veal CD, Trembath RC, Barker JN, Li C, Satten GA (2005).
Genetic Association Analysis Using Data from Triads and Unrelated Subjects.
Am. J. Hum. Genet., 76:592-608, 2005

famSKAT-RC 20140725 – Combining Family- and Population-based Imputation data for Association analysis of Rare and common Variants in large Pedigrees

famSKAT-RC 20140725

:: DESCRIPTION

famSKAT-RC is an R scripts to carry out a combined rare- and common-variant gene-based test of association in the presence of related individuals.

::DEVELOPER

Ellen M. Wijsman

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • R

:: DOWNLOAD

 famSKAT-RC

:: MORE INFORMATION

Citation:

Genet Epidemiol. 2014 Nov;38(7):579-90. doi: 10.1002/gepi.21844. Epub 2014 Aug 1.
Combining family- and population-based imputation data for association analysis of rare and common variants in large pedigrees.
Saad M1, Wijsman EM.

regioneR 1.24.0 – Association Analysis of Genomic Regions based on Permutation Tests

regioneR 1.24.0

:: DESCRIPTION

regioneR offers a statistical framework based on customizable permutation tests to assess the association between genomic region sets and other genomic features.

::DEVELOPER

Bernat Gel <bgel at imppc.org>

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / WIndows
  • R
  • BioCouductor

:: DOWNLOAD

 regioneR

:: MORE INFORMATION

Citation:

regioneR: an R/Bioconductor package for the association analysis of genomic regions based on permutation tests.
Gel B, Díez-Villanueva A, Serra E, Buschbeck M, Peinado MA, Malinverni R.
Bioinformatics. 2015 Sep 30. pii: btv562.

PLINK 1.90 b – Whole Genome Association Analysis Toolset

PLINK 1.90 b

:: DESCRIPTION

PLINK is a comprehensive toolset for statistical analysis in whole-genome association studies, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.

::DEVELOPER

Purcell Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac OsX / Windows

:: DOWNLOAD

PLINK

:: MORE INFORMATION

Citation

Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MAR, Bender D, Maller J, Sklar P, de Bakker PIW, Daly MJ & Sham PC (2007)
PLINK: a toolset for whole-genome association and population-based linkage analysis.
American Journal of Human Genetics, 81.

Baypass 2.2 – Genome-Wide Scan for Adaptive Differentiation and Association Analysis with Population-specific Covariables

Baypass 2.2

:: DESCRIPTION

The package BayPass is a population genomics software which is primarily aimed at identifying genetic markers subjected to selection and/or associated to population-specific covariates (e.g., environmental variables, quantitative or categorical phenotypic characteristics).

::DEVELOPER

Centre de Biologie et Gestion des Populations (CBGP)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 Baypass

:: MORE INFORMATION

Citation

Genome-Wide Scan for Adaptive Divergence and Association with Population-Specific Covariates.
Gautier M.
Genetics. 2015 Dec;201(4):1555-79. doi: 10.1534/genetics.115.181453.

HLA-IMPUTER – HLA Imputation and Association analysis using Population-specific Reference Panels

HLA-IMPUTER

:: DESCRIPTION

HLA-IMPUTER implements the HIBAG algorithm for HLA allele imputation with different population specific reference panels, including a new Han Chinese reference panel derived from 10,689 samples.

::DEVELOPER

WANLING YANG’S GROUP IN BIOINFORMATICS @ University of Hong Kong

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

Bioinformatics. 2019 Apr 1;35(7):1244-1246. doi: 10.1093/bioinformatics/bty730.
HLA-IMPUTER: an easy to use web application for HLA imputation and association analysis using population-specific reference panels.
Shen JJ, Yang C, Wang YF, Wang TY, Guo M, Lau YL, Zhang X, Sheng Y, Yang W.

UNPHASED 3.1.7 – Association Analysis in Nuclear Families and Unrelated Subjects

UNPHASED 3.1.7

:: DESCRIPTION

UNPHASED is an application for performing genetic association analysis in nuclear families and unrelated subjects. It implements maximum-likelihood inference on haplotype and genotype effects while allowing for uncertain phase and missing genotypes. Many of the commonly performed analyses are provided including transmission/disequilbrium tests, global and individual tests for haplotypes, tests that account for associations of nearby loci, tests of gene-gene interaction, adjustments for environmental covariates, genotype tests, comparison of risk between different haplotypes, and permutation tests.

::DEVELOPER

Frank Dudbridge

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux/windows/MacOsX
  • Java

:: DOWNLOAD

 UNPHASED

:: MORE INFORMATION

Citation

Dudbridge F (2008)
Likelihood-based association analysis for nuclear families and unrelated subjects with missing genotype data.
Hum Hered 66:87-98

RAP – Association Analysis Approach to Biclustering

RAP

:: DESCRIPTION

RAP (Range-support Association Pattern) is an novel approach based on association pattern analysis for discovering constant-row biclusters in gene expression data. Contrary to traditional association pattern discovery approaches, RAP works with real valued data sets without discritizing them. RAP discovers small highly coherent biclusters as opposed to large blocks discovered by traditional biclustering approaches.

::DEVELOPER

Data mining for biomedical informatics at the UMN

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

 RAP

:: MORE INFORMATION

AAOT — Association Analysis of an Ordinal Trait

AAOT

:: DESCRIPTION

AAOT (Association Analysis of an Ordinal Trait) is an SAS program that converts an ordinal trait to a quantitative trait, and prepares a data set that can be fed into FBAT for association analysis.

::DEVELOPER

The Collaborative Center for Statistics in Science(C2S2)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 AAOT

:: MORE INFORMATION

References

  1. Zhang H, Wang X, and Ye Y. Detection of genes for ordinal traits in nuclear families and a unified approach for association studies. Genetics, 172, 693-699, 2006.
  2. Wang X, Ye Y, and Zhang H. Family-based association tests for ordinal traits adjusting for covariates. Genetic Epidemiology, 30, 728-736, 2006.