Tag: TREAT

TREAT 0.0.5 – Detecting Complex Joint Effects in Case-control Studies

TREAT 0.0.5

:: DESCRIPTION

TREAT (TREe-based Association Test) version 0.0.5 is an R package for detecting complex joint effects in case-control studies. The test statistic is derived from a tree-structure model by recursive partitioning the data. Ultra-fast algorithm is designed to evaluate the significance of association between candidate gene and disease outcome.

::DEVELOPER

The Division of Cancer Epidemiology and Genetics (DCEG)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • R package

:: DOWNLOAD

 TREAT

:: MORE INFORMATION

Citation

Bioinformatics. 2014 May 2. [Epub ahead of print]
A fast and powerful tree-based association test for detecting complex joint effects in case-control studies.
Zhang H1, Wheeler W, Wang Z, Taylor PR, Yu K.

TREAT 1.0.1 – Targeted RE-sequencing Annotation Tool

TREAT 1.0.1

:: DESCRIPTION

TREAT ( Targeted RE-sequencing Annotation Tool) offers an comprehensive, open framework, end-to-end solution for analyzing and interpreting targeted re-sequencing data. TREAT encompasses sequence alignment, variant calling, variant annotation, variant filtering, and visualization in one comprehensive analytic workflow. The rich set of annotations provided by TREAT enables the filtering of detected variants based on their functional characteristics, and visualizations at the variant positions allow the investigators to closely examine the identified variants of interest

::DEVELOPER

Bioinformatics Program, Division of Biomedical Statistics and Informatics, Mayo Clinic Research

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 TREAT

:: MORE INFORMATION

Citation:

TREAT: a bioinformatics tool for variant annotations and visualizations in targeted and exome sequencing data.
Asmann YW, Middha S, Hossain A, Baheti S, Li Y, Chai HS, Sun Z, Duffy PH, Hadad AA, Nair A, Liu X, Zhang Y, Klee EW, Kalari KR, Kocher JP.
Bioinformatics. 2012 Jan 15;28(2):277-8. Epub 2011 Nov 15.