LTSOFT 3.0 – Analysis of Case-control Association Studies with known Risk Variants

LTSOFT 3.0

:: DESCRIPTION

LTSOFT is a software suite designed to more powerfully leverage clinical-covariates such as age, bmi, smoking status, and gender as well as genetic-covariates such as known associated variants when conducting case-control association studies. Including these covariates in standard regression models is not only suboptimal, but can in many instances reduce power.

::DEVELOPER

Alkes Price

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 LTSOFT

:: MORE INFORMATION

Citation:

Bioinformatics. 2012 Jul 1;28(13):1729-37. doi: 10.1093/bioinformatics/bts259. Epub 2012 May 3.
Analysis of case-control association studies with known risk variants.
Zaitlen N, Pasaniuc B, Patterson N, Pollack S, Voight B, Groop L, Altshuler D, Henderson BE, Kolonel LN, Le Marchand L, Waters K, Haiman CA, Stranger BE, Dermitzakis ET, Kraft P, Price AL.

EM-SNP – Allele Frequency Estimation, SNP Detection and Association Studies

EM-SNP

:: DESCRIPTION

EM-SNP is an unified approach for allele frequency estimation, SNP detection and association studies based on pooled sequencing data using EM algorithms

::DEVELOPER

Fengzhu Sun

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • R

:: DOWNLOAD

  EM-SNP

:: MORE INFORMATION

Citation

Quan Chen and Fengzhu Sun (2013):
A unified approach for allele frequency estimation, SNP detection and association studies on pooled sequencing data using EM algorithms.
BMC Genomics. 2013;14 Suppl 1:S1. doi: 10.1186/1471-2164-14-S1-S1.

SEQPower 1.0RC1 – Power Analysis for Sequence-based Association Studies

SEQPower 1.0RC1

:: DESCRIPTION

SEQPower provides statistical power analysis and sample size estimation for sequence-based association studies

::DEVELOPER

SEQPower team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX

:: DOWNLOAD

  SEQPower

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Apr 28. pii: btu296. [Epub ahead of print]
Power analysis and sample size estimation for sequence-based association studies.
Wang GT, Li B, Lyn Santos-Cortez RP, Peng B, Leal SM.

LDsplit – Association Studies of Recombination Hotspots using SNPs

LDsplit

:: DESCRIPTION

LDsplit is an open source Java program that detects SNPs (single nulceotide polymorphisms) associated with meiotic recombination hotspots.

::DEVELOPER

Jie Zheng, Ph.D.

:: SCREENSHOTS

LDsplit

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Java

:: DOWNLOAD

 LDsplit

:: MORE INFORMATION

Citation:

LDsplit: screening for cis-regulatory motifs stimulating meiotic recombination hotspots by analysis of DNA sequence polymorphisms.
Yang P, Wu M, Guo J, Kwoh CK, Przytycka TM, Zheng J.
BMC Bioinformatics. 2014 Feb 17;15:48. doi: 10.1186/1471-2105-15-48.

EINVis 20121021 – A Visualization tool for Analyzing and Exploring Genetic Interactions in Large-scale Association Studies

EINVis 20121021

:: DESCRIPTION

EINVis (Epistasis Interaction Network Visualization) is ONLINE FREE software that allows users to visualize and explore the epistatic interaction networks. EINVis provides three different views: EIN Tree Ring View, EIN Matrix View, and LD Tree Ring View.

::DEVELOPER

Yubao Wu

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • Java Scripts

:: DOWNLOAD

 EINVis 

:: MORE INFORMATION

Citation

Genet Epidemiol. 2013 Nov;37(7):675-85. doi: 10.1002/gepi.21754. Epub 2013 Aug 11.
EINVis: a visualization tool for analyzing and exploring genetic interactions in large-scale association studies.
Wu Y1, Zhu X, Chen J, Zhang X.

THESIAS 3.1 – Testing Haplotype Effects In Association Studies

THESIAS 3.1

:: DESCRIPTION

The objectif of the THESIAS program is to performed haplotype-based association analysis in unrelated individuals. This program is based on the maximum likelihood model.THESIAS allows one to simultaneous estimate haplotype frequencies and their associated effects on the phenotype of interest. In this new THESIAS release, quantitative, qualitative (logistic and matched-pair analysis), categorical and survival outcomes can be studied. X-linked haplotype analysis is also feasible.

::DEVELOPER

Tregouet David <tregouet@chups.jussieu.fr>
Garelle Valérie (garelle@chups.jussieu.fr)

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/Linux
  • Java

:: DOWNLOAD

  THESIAS

:: MORE INFORMATION

Citation

Tregouet DA, Garelle V.
A new JAVA interface implementation of THESIAS: Testing Haplotypes EffectS In Association Studies.
Bioinformatics. 2007;23(8):1038-1039.

QUANTO 1.2.4 – Computes Sample Size or Power for Association Studies

QUANTO 1.2.4

:: DESCRIPTION

Quanto is a program that computes sample size or power for association studies of genes, environmental factors, gene-environment interaction, or gene-gene interaction. Available study designs for a disease (binary) outcome include the unmatched case-control, matched case-control, case-sibling, case-parent, and case-only designs. Study designs for a quantitative tra it include independent individuals and case parent designs.

::DEVELOPER

W. James Gauderman

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 QUANTO

:: MORE INFORMATION

Citation

Gauderman (2002),
Sample size requirements for matched case-control studies of gene-environment interaction“,
Statistics in Medicine, 21:35-50.

GECOR – Power for Gene-Environment Interaction Tests in Matched Case-Control Association Studies

GECOR

:: DESCRIPTION

GECOR is a software for calculating sample sizes in matched case-control studies examining genetic and environmental factors,and/or gene-environment interaction. It allows for sample size calculations for the main effects of geneand/or environment, as well as gene-environment interaction.

::DEVELOPER

Peter Kraft

:: SCREENSHOTS

GECOR

:: REQUIREMENTS

  • Linux /  MacOsX/ Windows
  • java
  • R package

:: DOWNLOAD

 GECOR

:: MORE INFORMATION

HapMap filter 1.0 – Preprocess the HapMap Genotypic data for Association Studies

HapMap filter 1.0

:: DESCRIPTION

HapMap filter is a tool to preprocess the HapMap genotypic data for association studies.

::DEVELOPER

Dr. Wei Zhang, wzhang1@uchicago.edu

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • C++ Compiler

:: DOWNLOAD

 HapMap filter

:: MORE INFORMATION

Citation

HapMap filter 1.0: a tool to preprocess the HapMap genotypic data for association studies.
Zhang W, Duan S, Dolan ME.
Bioinformation. 2008 May 13;2(8):322-4.