MASA 1.0.0 – Multi-threshold (and Multi-marker) Association Study Analysis

MASA 1.0.0

:: DESCRIPTION

MASA is a new association testing method incorporating prior information to increase power.

::DEVELOPER

MASA team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsx/WIndows
  • Java

:: DOWNLOAD

 MASA

:: MORE INFORMATION

Citation:

Bioinformatics. 2012 Jun 15;28(12):i147-53. doi: 10.1093/bioinformatics/bts235.
Incorporating prior information into association studies.
Darnell G1, Duong D, Han B, Eskin E.

LMM-Lasso – Lasso Multi-Marker Mixed Model for Association Mapping with Population Structure Correction

LMM-Lasso

:: DESCRIPTION

LMM-Lasso is a linear mixed models that allows for both multi-locus mapping and correction for confounding effects.

::DEVELOPER

Machine Learning and Computational Biology Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Python

:: DOWNLOAD

 LMM-Lasso

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Jan 15;29(2):206-14. doi: 10.1093/bioinformatics/bts669.
A Lasso multi-marker mixed model for association mapping with population structure correction.
Rakitsch B, Lippert C, Stegle O, Borgwardt K.

TRIMM – TRIad Multi-Marker

TRIMM

:: DESCRIPTION

The TRIMM (TRIad Multi-Marker) program performs max_Z2, and sum_log(P) tests, association tests for a child’s or mother’s genetic effects using multiple markers from triad families. Statistical significance is evaluated via permutation. It also outputs the nominated risk-haplotype-tagging alleles

::DEVELOPER

Min Shi, M.D., Ph.D.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 TRIMM

:: MORE INFORMATION

Citation:

Shi M, Umbach DM ,Weinberg CR
Identification of Risk-related Haplotypes Using Multiple SNPs from Nuclear Families“.
The American Journal of Human Genetics, Volume 81, Issue 1, 53-66, 1 July 2007

GEI-TRIMM – Gene-environment Interaction Triad Multi-marker Method

GEI-TRIMM

:: DESCRIPTION

GEI-TRIMM(gene-environment interaction triad multi-marker method) is a software of testing haplotype-environment interactions using case-parent triads

::DEVELOPER

Min Shi, M.D., Ph.D.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 GEI-TRIMM

:: MORE INFORMATION

Citation:

Shi M, Umbach DM, Weinberg CR 2010
Testing Haplotype-Environment Interactions Using Case-parent Triads.”
Hum Hered. 2010;70(1):23-33. Epub 2010 Apr 23.