:: DESCRIPTION
HapCART is a convenient analysis tool for detecting disease-related haplotype-haplotype interactions. HapCART overcome high-dimensional issues which combine the advantages of data mining with the concept of haplotypes and consider haplotype uncertainty.
::DEVELOPER
Cathy S.J. Fann lab,Institute of Biomedical Informatics, National Yang-Ming University, Taipei
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
TOROCOR is designed (1) to characterise the spatial autocorrelation of quantitative and/or qualitative variables and (2) to test the significance of the association between variables, notably using torus-translation randomisations. The latter procedure removes the bias of classical tests applied on spatially autocorrelated variables where samples cannot be considered as independent (classical tests tend to be liberal, i.e. rejecting too often the null hypothesis that there is no association between variables).
::DEVELOPER
Olivier Hardy @ Evolutionary Biology & Ecology, Université Libre de Bruxelles
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
SQTDT / SPDT is an efficient and reliable algorithm for the semiparametric family-based tests of association.
::DEVELOPER
:: SCREENSHOTS
N/A
::REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
HAP-SAMPLE is an application for simulating SNP genotypes for case-control and affected-child trio studies by resampling from Phase I/II HapMap SNP data. The user provides a list of SNPs to be “genotyped,” along with a disease model file that describes causal SNPs and their effect sizes. The simulation tool is appropriate for candidate regions or whole-genome scans.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: MORE INFORMATION
Citation
Wright, F.A, Huang, H., Guan, X., Gamiel, K, Jeffries, C., Barry, W.T., de Villena, F.P., Sullivan, P.F., Wilhelmsen, K.C., and Zou. F. (2007)
Simulating association studies: a data-based resampling method for candidate regions or whole genome scans,
Bioinformatics 23: 2581-2588.
:: DESCRIPTION
tmax is a program for performing association analysis on a set of linked loci within a targeted region. It has 2 optional approaches, TMAX and SMAX, which are based on single locus test statistics (the log odds ratio) computed for each measured locus. TMAX utilizes the maximum of this series of test statistics, correcting for multiple testing by permutation of case-control status. SMAX utilizes the maximum of a smoothed curve fitted to the series of of test statistics. Again, the p-value is determined by permutation of case-control status.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Roeder, Bacanu, Sonpar, Zhang, and Devlin.
“Analysis of Single-Locus Tests to Detect Gene/Disease Associations”
Genet Epidemiol. 2005 Apr;28(3):207-19.
:: DESCRIPTION
CLUMPHAP implements a novel method for association testing based on clustering similar haplotypes (Knight et al. Submitted). This represents an extension of the basic methodology used in CLUMP, a program designed for the analysis of multi-allelic markers (Sham and Curtis 1995). CLUMPHAP calculates chi-squared statistics for binary partitions of haplotypes, where the number of partitions is reduced by allowing only those that are supported by a hierarchical cluster analysis of the haplotypes. CLUMPHAP obtains the empirical significance level of the largest chi-square statistic by a permutation procedure in which multiple permuted datasets (where the case-control labels have been randomly re-assigned) are subjected to exactly the same procedure of haplotype partitioning and calculation of largest chi-square statistic. Incidentally, this permutation procedure accounts for not only the inflation of the test statistic due to the maximization over the multiple ways of partitioning the haplotypes, but also for the uncertainty in haplotype phase of the individual subjects (Curtis and Sham 2006). The results are easy to interpret, a significant result suggests that a disease causing variant is present on haplotypes in the group which has an increased overall frequency in cases. CLUMPHAP reports the cluster pattern that resulted in the highest chi-squared along with the corresponding statistic and the empirical p-value.
::DEVELOPER
:: SCREENSHOTS
Command Line
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Knight J, Curtis D, Sham PC (submitted)
CLUMPHAP: A simple tool for performing haplotype-based association analysis.
Genet Epidemiol. 2008 Sep;32(6):539-45.
:: DESCRIPTION
DAPPLE looks for significant physical connectivity among proteins encoded for by genes in loci associated to disease according to protein-protein interactions reported in the literature. The hypothesis behind DAPPLE is that causal genetic variation affects a limited set of underlying mechanisms that are detectable by protein-protein interactions.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Rossin EJ, Lage K, Raychaudhuri S, Xavier RJ, Tartar D, IIBDGC, Cotsapas C, Daly MJ. 2011
Proteins Encoded in Genomic Regions Associated with Immune-Mediated Disease Physically Interact and Suggest Underlying Biology.
PLoS Genetics 7(1): e1001273
:: DESCRIPTION
The PDT (Pedigree Disequilibrium Test)analysis program allows the user to evaluate evidence of linkage disequilibrium (LD) in general pedigree data. All family data may be used without nullifying the validity of the association test, even when there is more than one affected in a family. The PDT program performs both allele-specific and genotype-specific LD analysis of individual markers. Version 5.1 adds the ability to perform genotype-specific analysis over marker sets.Â
::DEVELOPER
Duke Molecular Physiology Institute
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Eden R. Martin, S. Monks, L. Warren, N. Kaplan (2000)
A Test for Linkage and Association in General Pedigrees:The Pedigree Disequilibrium Test.
Am. J. Hum. Genet. 67:146-154, 2000
:: DESCRIPTION
The OSACC (Ordered Subset Analysis for Case-Control data) program was designed to evaluate evidence for association in the presence of genetic heterogeneity.
::DEVELOPER
Duke Molecular Physiology Institute
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Qin X, Hauser ER, Schmidt S.
Ordered Subset Analysis for Case-Control Studies
Genetic Epidemiology 34(5), 407-417
:: DESCRIPTION
X-LRT is a suite of family-based tests for detecting association of X-chromosome genes. This is a likelihood-based approach which can perform hypothesis testing as well as estimation of disease-related marker relative risks under a case-parent design. This test uses nuclear family with a single affected proband and allows additional siblings and missing parental genotypes. This program can test both single marker and haplotypes association.
::DEVELOPER
Duke Molecular Physiology Institute
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Zhang L, Martin ER, Chung RH, Li YJ, Morris RW. (2008)
X-LRT: a likelihood approach to estimate genetic risks and test association with X-linked markers using a case-parents design.
Genetic Epidemiology May;32(4):370-80.
