pvclust 2.0-0 – Hierarchical Clustering with P-values

pvclust 2.0-0

:: 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.

Comb-p 0.43 – Combining, Analyzing, Grouping and Correcting Spatially Correlated P-values

Comb-p 0.43

:: 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.

FastPval – Fast Two Stage P-value Computation Software

FastPval

:: DESCRIPTION

FastPval is a two stage p-value computation software which compute the empirical p-value by two stage ranking strategy, it can produce very low P-value based on huge dataset. This fast and powerful tool takes advantage of a delicate cutoff which separate the exactly significant area. Compared to the traditional ranking method, Tspvc has a good time efficiency, lower memory consuming and tiny storage spaces with high accuracy.

::DEVELOPER

Bioinformatics Group, HKU Department of Biochemistry

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOS
  • Java

:: DOWNLOAD

FastPval

:: MORE INFORMATION

Citation

Mulin Jun Li, Pak Chung Sham, and Junwen Wang
FastPval: a fast and memory efficient program to calculate very low P-values from empirical distribution.
Bioinformatics. 2010 Nov 15;26(22):2897-9. Epub 2010 Sep 21.

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

LDPAC 1.0.0 – Detect Spurious Associations using P-values

LDPAC 1.0.0

:: DESCRIPTION

LDPAC (LD-based Post-Association Cleaning) is a method for detecting spurious associations using p-values. The strength of the method is its simplicity; it requires no other information but p-values.

::DEVELOPER

Buhm Han

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 LDPAC

:: MORE INFORMATION

Citation

Buhm Han, Brian Hackel, Eleazar Eskin.
Postassociation cleaning using linkage disequilibrium information.
Genetic Epidemiology (2011) 35: 1–10.

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

TFM-Pvalue

:: 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
  • C++ Compiler

 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

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.

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.

efron 1.1 – Estimate the p-value in support of a Hypothesis of Recombination

efron 1.1

:: DESCRIPTION

 efron is a program written in C to estimate the p-value in support of a hypothesis of recombination among aligned nucleotide sequence data.

::DEVELOPER

Dorman Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C Compiler

:: DOWNLOAD

 efron

:: MORE INFORMATION

Citation

Dorman KS, Kaplan AH, Sinsheimer JS (2002)
Bootstrap confidence levels for HIV-1 recombination.
J. Mol. Evol. 54(2):200-209.

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.