:: DESCRIPTION
GECOR is a software for calculating sample sizes in matched case-control studies examining genetic and environmental factors,and/or gene-environment interaction. It allows for sample size calculations for the main effects of geneand/or environment, as well as gene-environment interaction.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
MDSOutlier is a free, open-source whole-genome case-control association analysis program, designed for systematic removal of outliers to reduce heterogeneity.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Shen Y, Liu Z, Ott J:
Systematic removal of outliers to reduce heterogeneity in case-control association studies.
Hum Hered 2010;70:227-231
:: DESCRIPTION
SPREG is a computer program for performing regression analysis of secondary phenotype data in case-control association studies. Secondary phenotypes are quantitative or qualitative traits other than the case-control status. Because the case-control sample is not a random sample of the general population, standard statistical analysis of secondary phenotype data can yield very misleading results.
::DEVELOPER
:: SCREENSHOTS
N/A
::REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Lin DY, Zeng D. 2009,
Proper analysis of secondary phenotype data in case-control association studies,
Genetic Epidemiology, 33:256-265.
:: DESCRIPTION
CNVineta is a flexible data mining tool for the analysis of copy number variations (CNVs) in large case-control SNP array data sets. The tool is available as an R statistical package. CNVineta offers a flexible and fast access to CNVs by a quick graphical overview in large case-control datasets. In addition, CNVineta provides rapid access to the log2 of raw data ratios (LRR) and B-allele frequencies (BAF) of specific or all samples, thereby allowing for a fast verification of the underlying raw data. CNVineta is also equipped with analysis methods for genome-wide screening for associated rare as well as common CNVs. Hence, CNVineta is a unique data mining tool to rapidly explore CNVs in large case-control data sets.
::DEVELOPER
Institute for Clinical Molecular Biology
:: SCREENSHOTS
N/A
::REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2010 Sep 1;26(17):2208-9. Epub 2010 Jul 6.
CNVineta: a data mining tool for large case-control copy number variation datasets.
Wittig M, Helbig I, Schreiber S, Franke A.
:: DESCRIPTION
simGWAS is a fast method for simulation of large scale case-control GWAS (genome-wide association study) summary statistics
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Fortune MD, Wallace C.
simGWAS: a fast method for simulation of large scale case-control GWAS summary statistics.
Bioinformatics. 2019 Jun 1;35(11):1901-1906. doi: 10.1093/bioinformatics/bty898. PMID: 30371734; PMCID: PMC6546134.
:: DESCRIPTION
Chaplin (Case-control haplotype inference package.) is a software program for identifying specific haplotypes or haplotype features that are associated with disease using genotype data from a case-control study.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Epstein MP and Satten GA (2003).
Inference on haplotype effects in case-control studies using unphased genotype data.
Am. J. Hum. Genet. 73:1316-1329
Satten GA and Epstein MP (2004).
Comparison of prospective and retrospective methods for haplotype inference in case-control studies.
Genet Epidemiol. 2004 Nov; 27(3):192-201
:: DESCRIPTION
LRASSOC suite deals with the situation where we have a case-control sample of affected and unaffected individuals with their marker genotypes for 2 biallelic marker loci. These 2 marker loci may be in linkage disequilibrium with 1 or 2 biallelic disease susceptibility loci and therefore affect disease risk through association or may themselves be disease susceptibility loci. We are interested in modelling the effects of the genotype on the probability of disease risk in order to draw conclusions regarding the nature of the joint effect of the loci. Among the issues we may wish to investigate are whether either of the 2 loci actually has an effect on disease risk, the strength and statistical significance of any effect, the nature of such an effect e.g is the effect additive on some scale or do the alleles at the same loci interact in a dominance effect. We also want to compare single and joint locus models to investigate how the strength and significance of the effect of each locus is affected by the presence or absence of the other in a model and, a related point, whether the additive and dominance effects of two loci are independent or whether they interact (often called epistasis in this context).
::DEVELOPER
:: SCREENSHOTS
Command Line
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
North B.V., Sham P.C. and Curtis D.
“Application of logistic regression to case-control association studies involving two causative loci“,
Human Heredity (2005) 59: 79-87.
:: DESCRIPTION
HAPSIM is a program for generating case-control multi-locus genotype data under a specified disease model.
::DEVELOPER
:: SCREENSHOTS
Command Line
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
B.V. North, D. Curtis, P.G.Cassell, G.A.Hitman and P. C. Sham
Assessing optimal neural network architecture for identifying disease-associated multi-marker genotypes using a permutation test, and application to calpain 10 polymorphisms associated with diabetes.
Annals of Human Genetics 67: 348-356
:: DESCRIPTION
NNPERM is a neural network program for analysing case-control multi-locus genotype data using a permutation test.
::DEVELOPER
:: SCREENSHOTS
Command Line
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
B.V. North, D. Curtis, P.G.Cassell, G.A.Hitman and P. C. Sham
Assessing optimal neural network architecture for identifying disease-associated multi-marker genotypes using a permutation test, and application to calpain 10 polymorphisms associated with diabetes.
Annals of Human Genetics 67: 348-356
:: DESCRIPTION
LTSOFT is a software suite designed to more powerfully leverage clinical-covariates such as age, bmi, smoking status, and gender as well as genetic-covariates such as known associated variants when conducting case-control association studies. Including these covariates in standard regression models is not only suboptimal, but can in many instances reduce power.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Bioinformatics. 2012 Jul 1;28(13):1729-37. doi: 10.1093/bioinformatics/bts259. Epub 2012 May 3.
Analysis of case-control association studies with known risk variants.
Zaitlen N, Pasaniuc B, Patterson N, Pollack S, Voight B, Groop L, Altshuler D, Henderson BE, Kolonel LN, Le Marchand L, Waters K, Haiman CA, Stranger BE, Dermitzakis ET, Kraft P, Price AL.
