Kinship 20091112 – Estimate Kinship Coefficients for Case-control analyses in the presence of Cryptic Relatedness

Kinship 20091112

:: DESCRIPTION

Kinship is a software to carry out computations to estimate kinship coefficients for case-control analyses in the presence of cryptic relatedness

::DEVELOPER

Ellen M. Wijsman

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 Kinship

:: MORE INFORMATION

Citation:

Genet Epidemiol. 2009 Dec;33(8):668-78. doi: 10.1002/gepi.20418.
Case-control association testing in the presence of unknown relationships.
Choi Y1, Wijsman EM, Weir BS.

CNVtools 1.62.0 – Robust CNV Case Control and Quantitative Trait Association

CNVtools 1.62.0

:: DESCRIPTION

CNVtools is an R package for performing robust case control and quantitative trait association analyses of Copy Number Variants.

::DEVELOPER

Chris Barnes

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • R
  • BioConductor

:: DOWNLOAD

  CNVtools 

:: MORE INFORMATION

Citation

A robust statistical method for case-control association testing with Copy Number Variation.
Barnes C, Plagnol V, Fitzgerald T, Redon R, Marchini J, Clayton D, Hurles ME.
Nature Genetics, 2008 Oct;40(10):1245-52

CGEN 3.2.0 – Genetic Analysis of Case-Control Data

CGEN 3.2.0

:: DESCRIPTION

CGEN (Case-control.Genetics) is an R package for analyzing genetic data on case-control samples, with particular emphasis on novel methods for detecting Gene-Gene and Gene-Environment interactions.

::DEVELOPER

 DCEG

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows/MacOsX
  • R package
  • Bioconductor

:: DOWNLOAD

  CGEN

:: MORE INFORMATION

Citation

Am J Hum Genet. 2010 Mar 12;86(3):331-42. doi: 10.1016/j.ajhg.2010.01.026. Epub 2010 Mar 4.
Using principal components of genetic variation for robust and powerful detection of gene-gene interactions in case-control and case-only studies.
Bhattacharjee S, Wang Z, Ciampa J, Kraft P, Chanock S, Yu K, Chatterjee N.

LTSOFT 3.0 – Analysis of Case-control Association Studies with known Risk Variants

LTSOFT 3.0

:: 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

Alkes Price

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 LTSOFT

:: 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.

Chaplin 1.2.3 – Case-control Haplotype Inference package

Chaplin 1.2.3

:: 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

Epstein software

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

   Chaplin

:: 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

LRASSOC 1.1 – Analysis of Case-control Data for Diseases with Two Susceptiblity Loci

LRASSOC 1.1

:: 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

Bernard North

:: SCREENSHOTS

Command Line

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

LRASSOC

:: 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.

HAPSIM – Produce the Case-control Multilocus Genotype Data

HAPSIM

:: DESCRIPTION

HAPSIM is a program for generating case-control multi-locus genotype data under a specified disease model.

::DEVELOPER

Bernard North

:: SCREENSHOTS

Command Line

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

HAPSIM

:: 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

NNPERM 1.3 – Analyse Case-control Multi-locus Genotype Data

NNPERM 1.3

:: DESCRIPTION

NNPERM is a neural network program for analysing case-control multi-locus genotype data using a permutation test.

::DEVELOPER

Bernard North

:: SCREENSHOTS

Command Line

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

NNPERM

:: 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

CNVineta 1.0-1 – Data mining tool for large case-control copy number variation data sets

CNVineta 1.0-1

:: 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

 CNVineta

:: 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.

HapEvolution – Detect Gene-gene Interactions from Case-control Haplotype data

HapEvolution

:: DESCRIPTION

HapEvolution is a cooperative coevolutionary algorithm (CCA) to detect gene-gene interactions from case-control haplotype data; moreover, this algorithm can tolerate up to 15% missing/ambiguous positions in haplotype data arising during haplotype phasing from genotypes. Further, the algorithm can compute epistatic associations from genes spanning multiple chromosomes.

::DEVELOPER

Population Therapeutics Research Group

:: SCREENSHOTS

HapEvolution

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • Java

:: DOWNLOAD

  HapEvolution

:: MORE INFORMATION