Bernie Devlin

Software Distribution - Computational Genetics Program - University of Pittsburgh

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SOFTWARE

Our group uses the statistical package R for a lot of our programs. For a some hints on R please click here:

R Hints

Detecting Association With Networks Software

Detecting Association With Networks (DAWN) (Updated 12/16/2015)
DAWN (Detecting Association With Networks) is a statistical algorithm that uses a hidden Markov random eld (HMRF) model to discover risk genes from gene co-expression network estimated by partial neighborhood selection (PNS) algorithm.

cLogit Software

cLogit Association Test (Updated 11/15/2016)
This R function calculates an association statistic for a case-control contrast using conditional logistic regression, not currently a feature of Plink. The function, similar to --logit in plink, allows for different diagnoses, inclusion of covariates (within the context of family-based association), and different clustering of cases and controls to be used for conditioning. The implementation is designed to use multiple processors when available.
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cLogit Proband Pseudo Control Genotypes
This R function creates a plink binary dataset with the genotypes for a proband and pseudo-controls based on the genotypes of the proband and itís parents as described in Crossett et al. 2010. Pseudo-controls will have the same sex as probands. The function handles three distinct genetic models: additive genetic, paternal parent of origin, and maternal parent of origin. Association tests using conditional logistic regression can be performed on the output file using cLogitAssociationTest_v1.1.R

Trio Transmission Counts (Updated 11/15/2016)
In traditional association analysis of trio data using the FBAT software (http://www.hsph.harvard.edu/fbat/default.html) the number of transmitted alleles, non-transmitted alleles, and the number of informative families are reported. This R function allows the user the generate this information for trio data that has been analyzed using conditional logistic regression using the proband-pseudo-control analysis described in Crossett et al. 2010. The function handles three distinct genetic models: additive genetic, paternal parent of origin, and maternal parent of origin. The program was designed to be used in concert with cLogitProbandPseudoControlGenotypes_v1.R and cLogitAssociationTest_v1.1.R to provide a complete association analysis of trio data using logistic regression.

Gene-level Analysis of Family and Case-control Data

Transmission And De novo Association test (TADA) (Updated 1/25/2016)
TADA (Transmission And De novo Association test) is a Bayesian model that effectively combines data from de novo mutations, inherited variants in families, and standing variants in the population (identified with case-control studies).

Estimating Genetic Ancestry

GemTools: A fast and efficient approach to estimating genetic ancestry
GemTools provides computationally efficient tools for modeling genetic ancestry based in the SNP information. GemTools is a package of functions to help the user account for genetic ancestry of a large number of individuals using spectral graph theory and projections to break a large problem into smaller pieces and calculate genetic ancestry information efficiently, i.e., a divide and conquer (dac) strategy.


Older Software

If you are looking for older software from our group check out our older software page.