:: DESCRIPTION
APL (Association in the Presence of Linkage) provides a novel test for association in the presence of linkage using general pedigree data.
::DEVELOPER
Duke Molecular Physiology Institute
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Chung R-H, Hauser ER, Martin ER (2006)
The APL test: Extension to general nuclear families and haplotypes and examination of its robustness.
Human Heredity. 61(4):189-99.
:: DESCRIPTION
SIMLA (SIMulation of pedigree data for Linkage and Association studies) is a SIMulation program that generates data sets of families for use in Linkage and Association studies. It allows the user flexibility in specifying marker and disease placement, locus heterogeneity, disequilibrium between markers and between markers and disease loci. Output is in the form of a LINKAGE pedigree file and is easily utilized, either directly or with minimal reformatting, as input for various genetic analysis packages.
::DEVELOPER
Duke Molecular Physiology Institute
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Schmidt MA, Hauser ER, Martin ER, Schmidt S.
Extension of the SIMLA package for gener ating pedigrees with complex inheritance patterns: Environmental covariates, gene-gene and gene-environment interaction.
Stat Appl Genet Mol Biol 4(1): article 15, 2005.
:: DESCRIPTION
TASSEL (Trait Analysis by aSSociation, Evolution, and Linkage) is a software package which performs a variety of genetic analyses. The analyses include association mapping, diversity estimation and calculating linkage disequilibrium. The association analysis between genotypes and phenotypes can be performed by either a general linear model or a mixed linear model. The general linear model now allows users to analyze complex field designs, environmental interactions, and epistatic interactions. The mixed model is specially designed to handle polygenic effects at multiple levels of relatedness including pedigree information.
rTASSEL construct an R-based front-end to connect to a variety of highly used TASSEL methods and analytical tools.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
/ R
:: MORE INFORMATION
Citation
Bradbury PJ, Zhang Z, Kroon DE, Casstevens TM, Ramdoss Y, Buckler ES. (2007)
TASSEL: Software for association mapping of complex traits in diverse samples.
Bioinformatics 23:2633-2635.
:: DESCRIPTION
LHiSA is an algorithm dedicated to large-scale association studies which aims to identify segments of genome involved in a disease. It is based on Local Score statistic and an automatic selection of the significant segments.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Stat Appl Genet Mol Biol. 2006;5:Article22. Epub 2006 Sep 17.
Detecting local high-scoring segments: a first-stage approach for genome-wide association studies.
Guedj M, Robelin D, Hoebeke M, Lamarine M, Wojcik J, Nuel G.
:: DESCRIPTION
MultAssoc is a MATLAB software package for test of association of a disease with a group of SNPs after accounting for their interaction with another group of SNPs or environmental exposures. In addition to implementing two standard logistic regression based tests, the package implements a novel method, called TukAssoc, that uses the Tukey’s 1 d.f. model for interaction between two groups of covariates.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Chatterjee N., Kalaylioglu Z., Moslehi R., Peters U., Wacholder S. (2006).
Powerful multilocus tests of genetic association in the presence of gene-gene and gene-environment interactions.
American Journal of Human Genetics, Vol. 79, 1002-16.
:: DESCRIPTION
The GIST (Genotype-IBD Sharing Test) is a method for detecting association between marker genotypes and IBD sharing at the same locus. Such an association will indicate that the marker itself, or one in linkage disequilibrium with it, could account for the observed linkage signal (at least partially). The software can be used to analyze affected sibship data.
::DEVELOPER
:: SCREENSHOTS
N/A
::REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Li C, Scott LJ, Boehnke M. (2004)
Assessing Whether an Allele Can Account in Part for a Linkage Signal: The Genotype-IBD Sharing Test (GIST).
Am. J. Hum. Genet. 74:418-431
:: DESCRIPTION
PAINTOR (Probabilistic Annotation INtegraTOR) is a probabilistic framework that integrates association strength with genomic functional annotation data to improve accuracy in selecting plausible causal variants for functional validation.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Integrating functional data to prioritize causal variants in statistical fine-mapping studies.
Kichaev G, Yang WY, Lindstrom S, Hormozdiari F, Eskin E, Price AL, Kraft P,Pasaniuc B.
PLoS Genet. 2014 Oct 30;10(10):e1004722. doi: 10.1371/journal.pgen.1004722. eCollection 2014.
:: DESCRIPTION
BaTS (Bayesian Tip-Significance testing) is a package that allows the user to test for significant phylogeny-trait correlations whilst taking into account uncertainty arising from phylogenetic error, by integrating over the credible set of topologies produced by Bayesian phylogenetics programs such as BEAST or MrBayes. Null distributions are generated for statistics of phylogeny-trait association, and used to test the significance of the observed data. BaTS can also perform batch analyses of multiple data sets.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Parker J, Rambaut A, Pybus OG. 2008.
Correlating viral phenotypes with phylogeny: accounting for phylogenetic uncertainty.
Infection, Genetics and Evolution 8:239-46
:: DESCRIPTION
MT-HESS is a Bayesain hierarchical model that analyses the association between a large set of predictors, e.g. SNPs (single nucleotide polymorphisms), and many responses, e.g. gene expression, in multiple tissues, cells or conditions.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
MT-HESS: an efficient Bayesian approach for simultaneous association detection in OMICS datasets, with application to eQTL mapping in multiple tissues.
Lewin A, Saadi H, Peters JE, Moreno-Moral A, Lee JC, Smith KG, Petretto E, Bottolo L, Richardson S.
Bioinformatics. 2015 Oct 26. pii: btv568
:: DESCRIPTION
The RVFam package provides functions to perform single SNP association analyses and gene-based tests for continuous, binary and survival traits against sequencing data (e.g. exome chip) using family data.
::DEVELOPER
Ming-Huei Chen <mhchen at bu.edu> and Qiong Yang
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
RVFam: An R Package for Rare Variant Association Analysis with Family Data.
Chen MH, Yang Q.
Bioinformatics. 2015 Oct 27. pii: btv609.
