Tag: Permutation test

regioneR 1.24.0 – Association Analysis of Genomic Regions based on Permutation Tests

regioneR 1.24.0

:: DESCRIPTION

regioneR offers a statistical framework based on customizable permutation tests to assess the association between genomic region sets and other genomic features.

::DEVELOPER

Bernat Gel <bgel at imppc.org>

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / WIndows
  • R
  • BioCouductor

:: DOWNLOAD

 regioneR

:: MORE INFORMATION

Citation:

regioneR: an R/Bioconductor package for the association analysis of genomic regions based on permutation tests.
Gel B, Díez-Villanueva A, Serra E, Buschbeck M, Peinado MA, Malinverni R.
Bioinformatics. 2015 Sep 30. pii: btv562.

PBOOST – Parallel Permutation Tests in Genome-wide Association Studies

PBOOST

:: DESCRIPTION

PBOOST is a GPU based tool for parallel permutation tests in genome-wide association studies.

::DEVELOPER

Laboratory for Bioinformatics and Computational Biology, HKUST

:: SCREENSHOTS

PBOOST

:: REQUIREMENTS

:: DOWNLOAD

  PBOOST 

:: MORE INFORMATION

Citation:

PBOOST: a GPU-based tool for parallel permutation tests in genome-wide association studies.
Yang G, Jiang W, Yang Q, Yu W.
Bioinformatics. 2014 Dec 21. pii: btu840.

FASTEH+ / FASTEHPLUS – Model-free Analysis and Permutation Test(s) of Allelic Association

FASTEH+ / FASTEHPLUS

:: DESCRIPTION

FASTEHPLUS performs model-free analysis and permutation test(s) of allelic association based on EH  and EHPLUS (Zhao et al.2000). It uses marker genotypes from a group of unrelated individuals or a group of cases and a group of controls and employs gene-counting algorithm to estimate haplotype frequencies and output asymptotic and permutation test statistics. As yet it does not handle missing genotypes. Please check for GENECOUNTING program on this site if you wish to use individuals with missing genotypes in your analysis.

::DEVELOPER

Jing Hua Zhao

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • linux/Windows/

:: DOWNLOAD

 FASTEHPLUS

:: MORE INFORMATION

Citation

Zhao, J. H., Sham, P. C. (2002)
“Faster allelic association analysis using unrelated subjects“.
Human Heredity, 53(1), 36-41.

EH+ / EHPLUS 2.0 – Model-free Analysis and Permutation tests for Allelic Association

EH+ / EHPLUS 2.0

:: DESCRIPTION

EHPLUS is a modified version of EH which only uses counts of genotypes that are actually observed. Each row of the data file consists of an identifying number for the genotype in question together with counts of the number of times it occurs in cases and controls. The genotype number is calculated in a similar way as for the original EH, and this number is produced automatically by PMPLUS, a program which accepts input files in the same format as PM but which outputs data in the format to be used by EHPLUS. EHPLUS also has a special method for handling memory requirement, which means that it can successfully deal with far more possible haplotypes than EH.

::DEVELOPER

Jing Hua Zhao

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • linux/Windows/

:: DOWNLOAD

  EHPLUS

:: MORE INFORMATION

Citation

Zhao, Curtis, Sham (2000),
“Model-free and permutation tests for allelic associations“,
Human Heredity, 50(2):133-139.