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.

regioneR 1.0.3 – Association Analysis of Genomic Regions based on Permutation Tests

regioneR 1.0.3

:: 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.

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.

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

SMARTscan 1.0 – Variable Grouping, Model Selection, Association Analysis of Microbiome Sequece data

SMARTscan 1.0

:: DESCRIPTION

SMARTscan (SMART-scan, scanning method of Selection of Models for the Analysis of Risk factor Trees ) is a taxa tree based variable grouping and model selection method for identifying phenotype-assocaited microbiome variables.

::DEVELOPER

Qunyuan Zhang, Ph.D.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • R

:: DOWNLOAD

 SMARTscan

:: MORE INFORMATION

Citation:

Selection of Models for the Analysis of Risk-factor Trees: Leveraging biological knowledge to mine large sets of risk factors with application to microbiome data.
Zhang Q, Abel H, Wells A, Lenzini P, Gomez F, Province MA, Templeton AA, Weinstock GM, Salzman NH, Borecki IB.
Bioinformatics. 2015 Jan 6. pii: btu855

GFlasso – Association Analysis that Searches for Genetic Variation

GFlasso

:: DESCRIPTION

GFlasso (graph-guided fused lasso) is a software for association analysis that searches for genetic variations influencing a group of correlated traits.

::DEVELOPER

the SAILING lab (the Laboratory of Statistical Artificial InteLligence and INtegrative Genomics)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Matlab
  • C Compiler

:: DOWNLOAD

 GFlasso

:: MORE INFORMATION

Citation

A multivariate regression approach to association analysis of a quantitative trait network.
Kim S, Sohn KA, Xing EP.
Bioinformatics. 2009 Jun 15;25(12):i204-12.

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.

GCPROG 2.6 – Association Analysis with Multiple Markers

GCPROG 2.6

:: DESCRIPTION

GCPROG is a support programs for GENECOUNTING to carry out association analyses with multiple markers.

::DEVELOPER

Dave Curtis

:: SCREENSHOTS

Command Line

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

GCPROG

:: MORE INFORMATION

GenABEL 1.8-0 – Genome-wide SNP Association Analysis

GenABEL 1.8-0

:: DESCRIPTION

GenABEL is a package for genome-wide association analysis between quantitative or binary traits and single-nucleotide polymorphisms (SNPs).

::DEVELOPER

GenABEL Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 GenABEL

:: MORE INFORMATION

Citation

Bioinformatics. 2007 May 15;23(10):1294-6. Epub 2007 Mar 23.
GenABEL: an R library for genome-wide association analysis.
Aulchenko YS, Ripke S, Isaacs A, van Duijn CM.