LSR – Estimate Region-specific p-values in Genetic Association Mapping studies

LSR

:: DESCRIPTION

LSR (Longest Run Test) is an S-plus program computes the distribution and the first moment of the length of the longest k-interrupted run (Lk) in a binary sequence.

::DEVELOPER

Cathy S.J. Fann lab,Institute of Biomedical Informatics, National Yang-Ming University, Taipei

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
S-plus

:: DOWNLOAD

LSR

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2008 May 27;9:246. doi: 10.1186/1471-2105-9-246.
Using the longest significance run to estimate region-specific p-values in genetic association mapping studies.
Lian IeB, Lin YH, Lin YC, Yang HC, Chang CJ, Fann CS.

TATES – multivariate GWAS based on P-values from GWAS

TATES

:: DESCRIPTION

TATES uses p-values as input and evaluates the evidence that at least one phenotype from multiple phenotypes is associated with a SNP.

::DEVELOPER

CTG (Complex Traits Genetics) Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows / Linux / MacOSX
Fortran Compiler

:: DOWNLOAD

TATES

:: MORE INFORMATION

Citation

PLoS Genet. 2013;9(1):e1003235. doi: 10.1371/journal.pgen.1003235. Epub 2013 Jan 24.
TATES: efficient multivariate genotype-phenotype analysis for genome-wide association studies.
van der Sluis S1, Posthuma D, Dolan CV.

ARTP 2.0.9.45 – Gene and Pathway p-values computed using the Adaptive Rank Truncated Product

ARTP 2.0.9.45

:: DESCRIPTION

ARTP (Adaptive Rank Truncated Product) is an R package for analyzing pre-defined genetic pathway based on a genetic association study.

::DEVELOPER

DCEG

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux/Windows/MacOsX
R package

:: DOWNLOAD

ARTP

:: MORE INFORMATION

Citation

Cancer Res. 2010 Jun 1;70(11):4453-9. doi: 10.1158/0008-5472.CAN-09-4502. Epub 2010 May 11.
Pathway analysis of breast cancer genome-wide association study highlights three pathways and one canonical signaling cascade.
Menashe I, Maeder D, Garcia-Closas M, Figueroa JD, Bhattacharjee S, Rotunno M, Kraft P, Hunter DJ, Chanock SJ, Rosenberg PS, Chatterjee N.

scaleboot 1.0-1 – Approximately Unbiased P-values via Multiscale Bootstrap

scaleboot 1.0-1

:: DESCRIPTION

scaleboot is an add-on package of R. This is for calculating approximately unbiased (AU) p-values from a set of multiscale bootstrap probabilities for a hypothesis.

::DEVELOPER

Shimodaira Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows / MacOsX
R package

:: DOWNLOAD

scaleboot

:: MORE INFORMATION

FAPI 0.1 – Fast and Accurate P-value Imputation for Genetic Association

FAPI 0.1

:: DESCRIPTION

FAPI is a powerful multi-thread Java-based application developed to infer p-values of untyped Single-nucleotide polymorphisms (SNPs) through p-values of SNPs in LD with the untyped one. With similar imputation accuracy to other genotype imputation tools (including IMPUTEand MACH), FAPI is superfast, without requiring phases of reference genotypes and any sample raw genotypes.

::DEVELOPER

Precision Medicine Genomics Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows / Linux / MacOSX
Java

:: DOWNLOAD

FAPI

:: MORE INFORMATION

Citation

Eur J Hum Genet. 2016 May;24(5):761-6. doi: 10.1038/ejhg.2015.190. Epub 2015 Aug 26.
FAPI: Fast and accurate P-value Imputation for genome-wide association study
Johnny S H Kwan, Miao-Xin Li, Jia-En Deng , Pak C Sham

tpWY – t-statistics, p-values, and Westfall and Young step-down method

tpWY

:: DESCRIPTION

tpWY (t-statistics, p-values, and Westfall and Young step-down method) consists of software to implement the methods illustrated by Dudoit et al. (2000) to compute unadjusted and adjusted p-values for the t-statistics derived from a collection of two-channel microarray experiments

::DEVELOPER

the Computational Biology and Informatics Laboratory (in the Center for Bioinformatics at the University of Pennsylvania)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux/ MacOsX / Windows
C Compiler

:: DOWNLOAD

tpWY

:: MORE INFORMATION

P_ACT 1.2 – P-values: Adjustment for Correlated Tests

P_ACT 1.2

:: DESCRIPTION

p_ACT (P-values: Adjustment for Correlated Tests) is an R program that adjusts sets of up to 500 p-values from association tests between correlated traits and SNPs for multiple testing, accounting for the correlation between tests.

::DEVELOPER

Center for Statistical Genetics, University of Michigan

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows / Linux / MacOS
R package

:: DOWNLOAD

P_ACT

:: MORE INFORMATION

Citation

Conneely, K.N. and Boehnke, M. (2007)
So many correlated tests, so little time! Rapid adjustment of p-values for multiple correlated tests.
American Journal of Human Genetics 81:1158-1168.