Tag: Case-control

CGEN 3.28.0 – Genetic Analysis of Case-Control Data

CGEN 3.28.0

:: 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.

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.

HAPGEN 2.2.0 – Simulate Case Control Datasets at SNP Markers

HAPGEN 2.2.0

:: DESCRIPTION

HAPGEN simulates case control datasets at SNP markers. The new version can now simulate multiple disease SNPs on a single chromosome, on the assumption that each disease SNP acts independently and are in Hardy-Weinberg equilibrium. We also supply a R package that can simulate interaction between the disease SNPs.

::DEVELOPER

Jonathan Marchini

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • MacOsX /  Linux

:: DOWNLOAD

 HAPGEN

:: MORE INFORMATION

Citation

Chris C. A. Spencer, Zhan Su, Peter Donnelly, Jonathan Marchini (2009)
Designing Genome-Wide Association Studies: Sample Size, Power, Imputation, and the Choice of Genotyping Chip.
PLoS Genet 5(5).

CNVtools 134.6 – Robust CNV Case Control and Quantitative Trait Association

CNVtools 1.34.6

:: DESCRIPTION

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

::DEVELOPER

CNVtools team

:: 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

NetShift – Identification of Driver Nodes between Case-control Association networks

NetShift

:: DESCRIPTION

‘NetShift’ is a website to visualize community shufflings in microbial association networks between healthy and diseased states and identify ‘driver’ nodes observed between the states.

::DEVELOPER

NetShift team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • WEb browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Kuntal BK, Chandrakar P, Sadhu S, Mande SS.
‘NetShift’: a methodology for understanding ‘driver microbes’ from healthy and disease microbiome datasets.
ISME J. 2019 Feb;13(2):442-454. doi: 10.1038/s41396-018-0291-x. Epub 2018 Oct 4. PMID: 30287886; PMCID: PMC6331612.

MQLS 1.5 – Case-Control Association Testing with Related Individuals

MQLS 1.5

:: DESCRIPTION

MQLS (More Powerful Quasi-Likelihood Score Test)can handle arbitrary number of markers and samples and have other features that we found useful in our studies, such as pedigree checking and input/output formats. In addition to genotyped markers, this version can carry out association tests using imputed allele counts (“dosages”) generated by MACH and an empirical variance estimator.

::DEVELOPER

Liming Liang

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /  Windows / MacOsX
  • C Compier

:: DOWNLOAD

  MQLS

:: MORE INFORMATION

Reference

Thornton T., McPeek M. S. (2007)
Case-Control Association Testing with Related Individuals: A More Powerful Quasi-Likelihood Score Test.
Am J Hum Genet, 81, 321-337.

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

CC-QLS 1.3 – Case-Control Quasi-Likelihood Score test

CC-QLS 1.3

:: DESCRIPTION

CC-QLS (Case-Control Quasi-Likelihood Score test) is a program to test for association in case-control samples that include related individuals with known genealogy. The tests implemented in the program have been developed for large inbred pedigrees but are also suitable for studies in outbred populations in which some individuals are relatives.

::DEVELOPER

Mary Sara McPeek

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows/MacOSX
  • C Compiler

:: DOWNLOAD

 CC-QLS

:: MORE INFORMATION

Citation:

Bourgain, Hoffjan, Nicolae, Newman, Steiner, Walker, Reynolds, Ober, McPeek (2003),
“Novel case-control test in a founder population identifies p-selectin as an Atopy-susceptibility locus“,
American Journal of Human Genetics, 73(3):612-626

CoaCC 1.0.1 – Simulate Case-control Study using Coalescent Framework

CoaCC 1.0.1

:: DESCRIPTION

CoaCC simulates a case-control study using a coalescent framework. It assumes a haploid sample of cases and a second haploid sample of controls. Of these two samples the genealogy is generated, dependent on the user-specified population history. From this genealogy a distribution of marker-haplotypes is generated by allowing for marker-mutation and recombinations between marker and gene as well as between markers.

::DEVELOPER

Sebastian Zöllner @ the Center for Statistical Genetics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /  Windows / MacOsX
  • C Complier

:: DOWNLOAD

 CoaCC

:: MORE INFORMATION

If you use CoaCC please e-mail szoellne@umich.edu or fill out the registration form.