cpgen: Parallelized Genomic Prediction and GWAS

Frequently used methods in genomic applications with emphasis on parallel computing (OpenMP). At its core, the package has a Gibbs Sampler that allows running univariate linear mixed models that have both, sparse and dense design matrices. The parallel sampling method in case of dense design matrices (e.g. Genotypes) allows running Ridge Regression or BayesA for a very large number of individuals. The Gibbs Sampler is capable of running Single Step Genomic Prediction models. In addition, the package offers parallelized functions for common tasks like genome-wide association studies and cross validation in a memory efficient way.

AuthorClaas Heuer
Date of publication2015-09-15 08:35:30
MaintainerClaas Heuer <cheuer@tierzucht.uni-kiel.de>
LicenseGPL (>= 2)
Version0.1
https://github.com/cheuerde/cpgen

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Files in this package

cpgen
cpgen/src
cpgen/src/Makevars
cpgen/src/clmm.cpp
cpgen/src/printer_unix.h
cpgen/src/pedigree_stuff.h
cpgen/src/printer.h
cpgen/src/pedigree_stuff.c
cpgen/src/ctools.h
cpgen/src/cGWAS.cpp
cpgen/src/actools.cpp
cpgen/src/clmm
cpgen/src/clmm/function_base.h
cpgen/src/clmm/base_methods_abstract.h
cpgen/src/clmm/mcmc.h
cpgen/src/clmm/functions.h
cpgen/src/clmm/mt_sampler.h
cpgen/src/clmm/effects.h
cpgen/src/clmm/R_sampler.h
cpgen/src/clmm/mcmc_abstract.h
cpgen/src/clmm/base_methods.h
cpgen/src/clmm.h
cpgen/src/Makevars.win
cpgen/src/cGWAS.h
cpgen/NAMESPACE
cpgen/R
cpgen/R/clmm.R cpgen/R/cSSBR.R cpgen/R/cGWAS.R cpgen/R/ctools.R cpgen/R/zzz.R
cpgen/MD5
cpgen/DESCRIPTION
cpgen/man
cpgen/man/cscale_inplace.Rd cpgen/man/cpgen-package.Rd cpgen/man/crossprodop.Rd cpgen/man/cGWAS.emmax.Rd cpgen/man/cmaf.Rd cpgen/man/ccov.Rd cpgen/man/set_num_threads.Rd cpgen/man/ccross.Rd cpgen/man/rand_data.Rd cpgen/man/clmm.Rd cpgen/man/cGBLUP.Rd cpgen/man/cSSBR.Rd cpgen/man/cpgen-parallel.Rd cpgen/man/get_cor.Rd cpgen/man/check_openmp.Rd cpgen/man/csolve.Rd cpgen/man/get_num_threads.Rd cpgen/man/cscanx.Rd cpgen/man/cCV.Rd cpgen/man/cgrm.D.Rd cpgen/man/cGWAS.Rd cpgen/man/cgrm.Rd cpgen/man/cSSBR.setup.Rd cpgen/man/cgrm.A.Rd cpgen/man/ccolmv.Rd cpgen/man/get_pred.Rd cpgen/man/cpowop.Rd cpgen/man/get_max_threads.Rd

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