PTest 20130115 – Testing set of observed small P-values in GWAS

PTest 20130115

:: DESCRIPTION

PTest (Partition test) is a software for case-control genetic association studies in human gene mapping. The PTest is based on single-SNP p-values resulting from an association test, for example, the chi-square test comparing genotype or allele frequencies in cases and controls.

::DEVELOPER

Jurg Ott, Ph.D.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux

:: DOWNLOAD

 PTest

:: MORE INFORMATION

Citation

Challenging false discovery rate: a partition test based on p values in human case-control association studies.
Ott J, Liu Z, Shen Y.
Hum Hered. 2012;74(1):45-50. doi: 10.1159/000343752. Epub 2012 Nov 13.

ManhattanPlotter 1.4 – Create Manhattan Plots and qq plots from P-values obtained in Genomic Studies

ManhattanPlotter 1.4

:: DESCRIPTION

ManhattanPlotter is a visual application developed in JAVA that easily creates Manhattan plots and qq plots from p-values obtained in genomic studies.

::DEVELOPER

Carlos Morcillo Suarez

:: SCREENSHOTS

ManhattanPlotter

:: REQUIREMENTS

  • Linux/ WIndows/MacOsX
  • Java

:: DOWNLOAD

 ManhattanPlotter

:: MORE INFORMATION

Comb-p 0.50.2 – Combining, Analyzing, Grouping and Correcting Spatially Correlated P-values

Comb-p 0.50.2

:: DESCRIPTION

comb-p is a command-line tool and a python library that manipulates BED files of possibly irregularly spaced P-values and (1) calculates auto-correlation, (2) combines adjacent P-values, (3) performs false discovery adjustment, (4) finds regions of enrichment (i.e. series of adjacent low P-values) and (5) assigns significance to those regions.

::DEVELOPER

Katerina Kechris , Brent Pedersen

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux
  • Python

:: DOWNLOAD

 Comb-p

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Nov 15;28(22):2986-8. doi: 10.1093/bioinformatics/bts545. Epub 2012 Sep 5.
Comb-p: software for combining, analyzing, grouping and correcting spatially correlated P-values.
Pedersen BS1, Schwartz DA, Yang IV, Kechris KJ.

pvclust 2.2-0 – Hierarchical Clustering with P-values

pvclust 2.2-0

:: DESCRIPTION

pvclust is an R package for assessing the uncertainty in hierarchical cluster analysis. For each cluster in hierarchical clustering, quantities called p-values are calculated via multiscale bootstrap resampling. P-value of a cluster is a value between 0 and 1, which indicates how strong the cluster is supported by data.

::DEVELOPER

Shimodaira Group

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • R package

:: DOWNLOAD

 pvclust

:: MORE INFORMATION

Citation

Pvclust: an R package for assessing the uncertainty in hierarchical clustering.
Suzuki R, Shimodaira H.
Bioinformatics. 2006 Jun 15;22(12):1540-2. Epub 2006 Apr 4.

TFM-Pvalue 0.0.8 – Efficient and Accurate P-value Computation for Position Weight Matrices

TFM-Pvalue 0.0.8

:: DESCRIPTION

TFM-Pvalue is a software suite providing tools for computing the score threshold associated to a given P-value and the P-value associated to a given score threshold. It uses Position Weight Matrices, such as those available in the Transfac or Jaspar databases.

::DEVELOPER

Bonsai Bioinformatics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX/Windows
  • R

 TFM-Pvalue

:: MORE INFORMATION

Citation

Efficient and accurate P-value computation for Position Weight Matrices
H. Touzet and J.S. Varré
Algorithms for Molecular Biology 2007, 2:15

StatSigMA beta / StatSigMA-w v2 – Computes P-value of (Whole-Genome) Multiple Alignment

StatSigMA beta / StatSigMA-w v2

:: DESCRIPTION

StatSigMA (Statistical Significance of Multiple Alignments) computes the statistical significance of multiple sequence alignments (of either nucleotide or amino acid sequences), much as BLAST’s E-values provide statistical significance for pairwise alignments.

StatSigMA-w (Statistical Significance of Whole-Genome Multiple Alignments),Given any multiple sequence alignment and a phylogeny of the aligned sequences, assesses the accuracy of the alignment and identifies suspiciously aligned regions.

::DEVELOPER

The Computational & Synthetic Biology group – COMPUTER SCIENCE & ENGINEERING at UNIVERSITY OF WASHINGTON

:: SCREENSHOTS

Command Line

:: REQUIREMENTS

:: DOWNLOAD

StatSigMA , StatSigMA-w

:: MORE INFORMATION

Citation:

A. Prakash, M. Tompa,
Assessing the discordance of multiple sequence alignments“,
IEEE/ACM Trans Comput Biol Bioinform, vol. 6 (2009) 542-51.Pubmed 19875854.

X. Chen, M. Tompa,
Comparative assessment of methods for aligning multiple genome sequences“,
Nat. Biotechnol., vol. 28 (2010) 567-72.

DASS – Discovery and P-value Calculation of Substructures in Unordered data

DASS

:: DESCRIPTION

DASS (Discovery of All Significant Substructures) that first identifies all substructures in unordered data (DASSSub) in a manner that is especially efficient for modular data. In addition, DASS calculates the statistical significance of the identified substructures, for sets with at most one element of each type (DASSPset), or for sets with multiple occurrence of elements (DASSPmset).

::DEVELOPER

Dr. Maik Friedel , J.Hollunder

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux

:: DOWNLOAD

  DASS

:: MORE INFORMATION

Citation

DASS: Efficient Discovery and P-Value Calculation of Substructures in Unordered Data
Jens Hollunder, Maik Friedel, Andreas Beyer, Christopher T. Workman, Thomas Wilhelm
Bioinformatics (2007), 23(1): 77-83.

 

RTP – Calculate Significance of Truncated Products of P-values

RTP

:: DESCRIPTION

RTP: C code for calculating significance of truncated products of P-values

::DEVELOPER

Frank Dudbridge

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOS
  • C Compiler

:: DOWNLOAD

  RTP

:: MORE INFORMATION

Citation

Genet Epidemiol. 2003 Dec;25(4):360-6.
Rank truncated product of P-values, with application to genomewide association scans.
Dudbridge F, Koeleman BP.

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

GrASP 0.6 beta – Graphical Assessment of Sliding P-values

GrASP 0.6 beta

:: DESCRIPTION

GrASP (Graphical Assessment of Sliding P-values)  is a graphical tool to display and assess p-values from sliding window tests. It can present thousands of p-values from the sliding window tests as a simple graphic that uses varying levels of user-specified color to indicate the width of the sliding windows and the varying levels of significance. It therefore allows the user to identify regions/blocks of interest from these sliding windows, based jointly on the absolute p-value of the tests from these windows and the building of haplotypes of significance in the region. GrASP is executed as an Excel macro and is written in Excel’s built-in version of Visual Basic for Applications.

::DEVELOPER

Rasika Mathias @ NHGRI

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows
  • Excel
  • Perl

:: DOWNLOAD

 GrASP

:: MORE INFORMATION

Citation:

Mathias, R.A., Gao, P., Goldstein, J.L., Wilson, A.F., Pugh, E.W., Furbert-Harris, P., Dunston, G., Malveaux, F., Togias, A., Barnes, K.C., Beaty, T.H., Huang, S.K. 2006.
A graphical assessment of p-values from sliding window haplotype tests of association to identify asthma susceptibility loci on chromosome 11q.
BMC Genet. 14;7(1):38.