ARR 1.0 – Adaptive Ridge Regression for Rare Variant Detection

ARR 1.0

:: DESCRIPTION

ARR (adaptive ridge regression) is an R package to detect rare variants associated with a quantitative trait using the adaptive ridge regression method.

:: DEVELOPER

Xu’s Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX/Windows
  • R Package

:: DOWNLOAD

 ARR

:: MORE INFORMATION

Citation:

PLoS One. 2012;7(8):e44173. Epub 2012 Aug 28.
Adaptive ridge regression for rare variant detection.
Zhan H, Xu S.

ModuleMaster 1.1 – Identify Cis-regulatory Modules using Promoter Analysis and Microarray Expression data Regression

ModuleMaster 1.1

:: DESCRIPTION

ModuleMaster is a novel application for finding cis-regulatory modules (CRMs) in sets of co-expressed genes. The application comes with a newly developed method which not only considers transcription factor binding information but also multivariate functional relationships between regulators and target genes to improve the detection of CRMs. Given only the results of a microarray and a subsequent clustering experiment, the program includes all necessary data and algorithms to perform every step to find CRMs.

::DEVELOPER

the Center for Bioinformatics Tübingen (Zentrum für Bioinformatik Tübingen, ZBIT).

:: SCREENSHOTS

ModuleMaster

:: REQUIREMENTS

  • Linux/ WIndows/MacOsX
  • Java

:: DOWNLOAD

  ModuleMaster

:: MORE INFORMATION

Citation

Biosystems. 2010 Jan;99(1):79-81. doi: 10.1016/j.biosystems.2009.09.005. Epub 2009 Oct 9.
ModuleMaster: a new tool to decipher transcriptional regulatory networks.
Wrzodek C, Schröder A, Dräger A, Wanke D, Berendzen KW, Kronfeld M, Harter K, Zell A.

HTR – Haplotype Trend Regression

HTR

:: DESCRIPTION

HTR is an Haplotype/Trait Association Software.

::DEVELOPER

Dmitri Zaykin

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux

:: DOWNLOAD

 HTR

:: MORE INFORMATION

Citation:

Zaykin DV, Westfall PH, Young SS, Karnoub MC, Wagner MJ, Ehm MG (2002),
Testing association of statistically inferred haplotypes with discrete and continuous traits in samples of unrelated individuals“,
Human Heredity, 53:79-91.

ROMPrev 0.2.1 beta – Revised Regression of Offspring on Mid-Parent

ROMPrev 0.2.1 beta

:: DESCRIPTION

ROMPrev is a software suite for quantitative trait and locus-specific heritability estimation and association testing using the revised ROMP (Regression of Offspring on Mid-Parent) method.

:DEVELOPER

Alexander F. Wilson @ NHGRI

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / Unix
  • R Package

:: DOWNLOAD

  ROMPrev

:: MORE INFORMATION

Citation:

Roy-Gagnon, M.H., Mathias, R.A., Fallin, M.D., Jee, S.H., Broman, K.W., Wilson, A.F. 2008.
An extension of the regression of offspring on mid-parent to test for association and estimate locus-specific heritability: the revised ROMP method.
Ann Hum Genet. 72(Pt 1):115-25.