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Software

In their present form, these items of software are distributed as shareware. The statistical methods implemented have been or are in the process of being documented in the scientific literature.

2009

BSA, Bayesian Segmentation Approach (L Wu et all). BSA contains 4 files to run:

readme.pdf - BSA manual
BSA_library.txt - contains supporting functions
WGTP_DUP.txt - contains main function to identify duplications in HapMap data
WGTP_DEL.txt - contains main function to identify deletions in HapMap data

2007

elrm (D Zamar, J Graham, B McNeney 2007): An R package implementing Exact Logistic Regression via MCMC. Freely available from cran.r-project.org

luca (J Shin, B McNeney, J Graham 2007): An R package for case-control inference of statistical interaction between genetic and nongenetic risk factors under covariate assumptions. Freely available from cran.r-project.org

EMRF (SFF Lee, 2007) EM-Random Forest (EMRF) for Haseman-Elston quantitative trait linkage analysis accounts for marker ambiguity and weights each sib-pair according to the posterior identical by descent (IBD) distribution. New variable importance (VI) indices borrow information from linked markers using the correlation structure inherent in IBD linkage data.

The compiled C program for EMRF is freely available at http://fisher.utstat.toronto.edu/slee/EMRF. Source code is available upon request.

2005 - 2006

LDheatmap (Shin, Blay, McNeney, Graham 2006): An R function for graphical display of pairwise linkage disequilibria between single nucleotide polymorphisms. Journal of Statistical Software, 16: Code Snippet 3, 2006. Available from www.jstatsoft.org

hapassoc (Burkett, Graham, McNeney 2006): Software for likelihood inference of trait associations with SNP haplotypes and other attributes. Journal of Statistical Software 16(2), 2006. Available from www.jstatsoft.org

BR_Squared, version1.1 (Wu, Sun, Bull 2006): A set of PERL scripts that calculate selection-bias-reduced bootstrap estimates of locus-specific heritability of QTL using MERLIN-REGRESS. Available at http://www.mshri.on.ca/mitacs/software/BRsquared.HTML

GEE2loc, release 1 (Biernacka, Sun, Bull 2005a,b): FORTRAN software for point and interval estimation and hypothesis testing in a two-locus model for linked disease susceptibility genes. Available at http://individual.utoronto.ca/joanna_b/GEE2l.htm

QTsegr (Loredo-Osti, Morgan; Loredo-Osti et al 2005) Program to compute segregation of quantitative traits by mixture models taking into account fixed covariates, as well as perform joint linkage and segregation analysis on pedigrees without loops. Available at http://www.medicine.mcgill.ca/statgene/software.html

Currently Under Development

MiniPed (Löschner, Loredo-Osti, K Morgan): A C++ branch-and-bound algorithm to extract Steiner trees in large complex pedigrees.

cluspect (Tritchler et al, 2005) The spectral clustering method has been implemented in an R package, which we plan to publish. A method for estimating the number of clusters (Fallah et al, 2006) is included in the package.

HMM.hap (S Sun, R Neal, C Greenwood): Haplotype estimation using a hidden Markov model in population samples.

B Xing (Xing, Greenwood, Bull 2006): MATLAB code for hierarchical clustering of CGH data

S Colby (Mastracci et al 2006): R-code for identification of minimum common region of copy number alteration by post-processing of CGH data after circular binary segmentation analysis

JP Lewinger, SSF Lee, SB Bull. GAUSS functions to perform likelihood and penalized likelihood inference for unconditional logistic regression with sparse data.

W Xu, C Greenwood. Recursive partitioning algorithms for genetic linkage analysis.

Previously Available:

J Graham, B McNeney and F Seillier-Moiseiwitsch. stepwise: an R package and stand-alone C program for stepwise detection of recombination breakpoints in sequence alignments.

CMT Greenwood, L Mirea, SB Bull. LINKWCOV – software for affected sibpair linkage analyses with covariates and tests for heterogeneity.

Y Liu, D Tritchler. S-plus functions for transmission disequilibrium analysis of continuous and discrete traits (CTDT). http://www.uhnresearch.ca/labs/tritchler/

D Tritchler. S-plus functions for linkage analysis of complex models for discrete and continuous traits. http://www.uhnresearch.ca/labs/tritchler/

JC Loredo-Osti, K Morgan, Pedfiddler, a package of C/C++ programs for pedigree drawing. Available at http://www.medicine.mcgill.ca/statgene/software.html

JC Loredo, K Morgan. Parente, a program to compute Malecot’s kinship and inbreeding and Jacquard’s condensed identity-by-descent coefficients Available at http://www.medicine.mcgill.ca/statgene/software.html

JC Loredo-Osti, K Morgan. Imaqtl, a program to perform robust statistical QTL interval mapping on F2 crosses. Available at http://www.medicine.mcgill.ca/statgene/software.html

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