PRESTO 1.01 – Calculation of Order Statistic Distributions and Multiple-testing Adjusted P-values via Permutation

PRESTO 1.01

:: DESCRIPTION

PRESTO is optimized software for permutation testing and for computing empirical distributions of order statistics via permutation. PRESTO is extremely fast and can efficiently analyze data from one and two-stage whole genome association studies with millions of markers genotyped on thousands of samples.

::DEVELOPER

Brian L. Browning 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Java

:: DOWNLOAD

 PRESTO

:: MORE INFORMATION

Citation:

B L Browning (2008)
PRESTO: Rapid calculation of order statistic distributions and multiple-testing adjusted P-values via permutation for one and two-stage genetic association studies.
BMC Bioinformatics 9:309.

npGSEA 1.28.0 – Permutation Approximation methods for Gene Set Enrichment Analysis

npGSEA 1.28.0

:: DESCRIPTION

npGSEA  (non-permutation GSEA) calculates gene set enrichment statistics and p-values without the computational cost of permutations. It is applicable in settings where one or many gene sets are of interest. There are also built-in plotting functions to help users visualize results.

::DEVELOPER

Jessica Larson <larson.jess at gmail.com> and Art Owen

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/ MacOsX
  • R
  • BioConductor

:: DOWNLOAD

 npGSEA

:: MORE INFORMATION

Citation

Moment based gene set tests.
Larson JL, Owen AB.
BMC Bioinformatics. 2015 Apr 28;16(1):132.

BaobabLuna 1.1 beta – Manipulation of Signed Permutations in the Context of Genomic Evolution

BaobabLuna 1.1 beta

:: DESCRIPTION

BaobabLUNA is a java framework to deal with permutations that represent genomes in rearrangement analysis. baobabLUNA contains a collection of classes for building breakpoint graphs (the basic structures behind the work on genome rearrangements), performing reversals, calculating reversal distances, sorting permutations. Includes a text representation for the breakpoint graph.baobabLUNA is only able to deal with unichromosomal genomes and its main functionality is the implementation of an algorithm that gives a compact representation of the space of all solutions of the sorting by reversals problem, that is, a representation of all optimal sequences of reversals that sort one genome into another.

::DEVELOPER

Marília D. V. Braga

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows/MacOsX
  • Java

:: DOWNLOAD

 BaobabLuna

:: MORE INFORMATION

Citation

Braga M. D. V.,
baobabLUNA: the solution space of sorting by reversals,
Bioinformatics, vol. 25, no. 14, 1833–1835, 2009.

permuteP 1.4 – Permutation P-value Calculation

permuteP 1.4

:: DESCRIPTION

permuteP exacts permutation p-value calculation for case-control study of collapsoing a group of rare SNPs, and approximate permutation p-value calculation for QTL mapping in experimental cross

::DEVELOPER

Wei Sun

:: SCREENSHOTS

N/A

::REQUIREMENTS

:: DOWNLOAD

   permuteP

:: MORE INFORMATION