CNALR 1.0 – Stratification of Tumour Subtypes based on Copy Number Alteration Profiles

CNALR 1.0

:: DESCRIPTION

CNALR is an R package to perform a stratification of tumour subtypes based on copy number alteration profiles using next-generation sequence data. This webpage is currently set to support the submission of the manuscript Stratifying tumour subtypes based on copy number alteration profiles using next-generation sequence data

::DEVELOPER

Arief Gusnanto

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
R

:: DOWNLOAD

CNALR

:: MORE INFORMATION

Citation

Stratifying tumour subtypes based on copy number alteration profiles using next-generation sequence data.
Gusnanto A, Tcherveniakov P, Shuweihdi F, Samman M, Rabbitts P, Wood HM.
Bioinformatics. 2015 Apr 5. pii: btv191.

EIGENSOFT 7.2.1 – Population Structure , Eigenanalysis & Stratification

EIGENSOFT 7.2.1

:: DESCRIPTION

EIGENSOFT package combines functionality from our population genetics methods (Patterson et al. 2006) and our EIGENSTRAT stratification method (Price et al. 2006). The EIGENSTRAT method uses principal components analysis to explicitly model ancestry differences between cases and controls along continuous axes of variation; the resulting correction is specific to a candidate marker’s variation in frequency across ancestral populations, minimizing spurious associations while maximizing power to detect true associations. The EIGENSOFT package has a built-in plotting script and supports multiple file formats and quantitative phenotypes.

::DEVELOPER

Reich laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

EIGENSOFT

:: MORE INFORMATION

Citation:

Nature Genetics 38, 904 – 909 (2006) Published online: 23 July 2006; | doi:10.1038/ng1847
Principal components analysis corrects for stratification in genome-wide association studies
Alkes L Price, Nick J Patterson, Robert M Plenge, Michael E Weinblatt, Nancy A Shadick & David Reich

Population Structure and Eigenanalysis
Nick Patterson, Alkes L. Price, David Reich
December 2006 Issue of PLoS Genetics

BioBin 2.3.0 – Explore Rare Variant Population Stratification

BioBin 2.3.0

:: DESCRIPTION

BioBin meets a critical need for an improved binning algorithm through the advantage of prior biological knowledge and potential cumulative effects of biologically aggregated RVs. BioBin requires the Library of Knowledge Integration (LOKI), which contains diverse prior knowledge from multiple collections of biological data. BioBin can be used to apply multiple levels of burden collapsing/testing, including: regulatory regions, evolutionary conserved regions, genes, and/or pathways without a need for an external feature file. BioBin aids rare variant analysis by binning variants according to prior biological knowledge.

::DEVELOPER

Ritchie Lab

:: SCREENSHOTS

N/A

::REQUIREMENTS

Linux
C++ Compiler

:: DOWNLOAD

BioBin

:: MORE INFORMATION

Citation

Pac Symp Biocomput. 2013:332-43.
Using BioBin to explore rare variant population stratification.
Moore CB, Wallace JR, Frase AT, Pendergrass SA, Ritchie MD.

PSAT – Population Stratification Association Test

PSAT

:: DESCRIPTION

PSAT (Population Stratification Association Test) is a software for testing association between single nucleotide polymorphisms (SNPs) and a disease with stratification. Population stratification can be a serious obstacle in the analysis of genome-wide association studies. We have developed a method for evaluating the significance of association scores in whole-genome cohorts with stratification. Our approach is a randomization test akin to a standard permutation test. It conditions on the genotype matrix and thus takes account not only of the population structure but also of the complex linkage disequilibrium structure of the genome. As we show in simulation experiments, our method achieves higher power and significantly better control over false positive rates than existing methods. In addition, it can be easily applied to whole genome association studies.

::DEVELOPER

Ron Shamir’s lab

:: SCREENSHOTS

N/A

::REQUIREMENTS

Windows with Cygwin /Linux

:: DOWNLOAD

PSAT

:: MORE INFORMATION

Citation

A randomization test for controlling population stratification in whole-genome association studies
G. Kimmel, M.I. Jordan, E. Halperin, R. Shamir and R.M. Karp RM
American Journal of Human Genetics (2007) , Vol. 81 No. 5, 895-905 (2007)

PSIKO v2 – Infer Population Stratification on various levels in GWAS

PSIKO v2

:: DESCRIPTION

PSIKO (Population Structure Inference using Kernel-pca and Optimisation) is a software tool written in C++ for quick and accurate estimation of individual ancestry coefficients of a dataset exhibiting population structure.

::DEVELOPER

The UEA Computational Biology Laboratory at the University of East Anglia (UEA)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
g++

:: DOWNLOAD

PSIKO

:: MORE INFORMATION

Citation

PSIKO2: a fast and versatile tool to infer population stratification on various levels in GWAS.
Popescu AA, Huber KT.
Bioinformatics. 2015 Jul 2. pii: btv396.