Aberrant 1.0 – Indentify Outliers from otherwise Guassian Distributions

Aberrant 1.0

:: DESCRIPTION

Aberrant is a R package for automatically indentiying outliers from otherwise Guassian distributions. It is designed for excluding samples from genome-wide association studies which have summary statistics of variation which differ from the sample at large.

::DEVELOPER

Celine Bellenguez and Chris CA Spencer

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

   Aberrant

:: MORE INFORMATION

Citation

Celine Bellenguez, Amy Strange, Colin Freeman, Wellcome Trust Case Control Consortium 2, Peter J Donnelly and Chris CA Spencer. (2011)
A robust clustering algorithm for identifying problematic samples in genome-wide association studies.

STAC 1.2 – Significance Testing for Aberrant Copy-Number

STAC 1.2

:: DESCRIPTION

STAC (Significance Testing for Aberrant Copy-Number) is a method for testing the significance of DNA copy number aberrations across multiple array-CGH experiments. It utilizes two complementary statistics in combination with a novel search strategy. The significance of both statistics is assessed, and P-values are assigned to each location on the genome by using a multiple testing corrected permutation approach. STAC identifies genomic alterations known to be of clinical and biological significance and provides statistical support for 85% of previously reported regions. Moreover, STAC identifies numerous additional regions of significant gain/loss in these data that warrant further investigation. The P-values provided by STAC can be used to prioritize regions for follow-up study in an unbiased fashion.

::DEVELOPER

the Computational Biology and Informatics Laboratory (in the Center for Bioinformatics at the University of Pennsylvania)

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux/ MacOsX / Windows
  •  Java

:: DOWNLOAD

 STAC

:: MORE INFORMATION

Citation:

Diskin SJ, Eck T, Greshock J, Mosse YP, Naylor T, Stoeckert CJ Jr, Weber BL, Maris JM, Grant GR.
STAC: A method for testing the significance of DNA copy number aberrations across multiple array-CGH experiments
Genome Res. 2006 Sep;16(9):1149-58. Epub 2006 Aug 9.