Genome-Wide Association Study with SNP-Set Methods
c(
person("Kosuke", "Hamazaki", email = "hamazaki@ut-biomet.org", role = c("aut", "cre")),
person("Hiroyoshi", "Iwata", email = "aiwata@mail.ecc.u-tokyo.ac.jp", role = c("aut", "ctb"))
)
By using 'RAINBOWR' (Reliable Association INference By Optimizing Weights with R), users can test multiple SNPs (Single Nucleotide Polymorphisms) simultaneously by kernel-based (SNP-set) methods. This package can also be applied to haplotype-based GWAS (Genome-Wide Association Study). Users can test not only additive effects but also dominance and epistatic effects. In detail, please check our preprint on bioRxiv: Kosuke Hamazaki and Hiroyoshi Iwata (2019) <doi:10.1101/612028>.
Rcpp, rrBLUP, rgl, tcltk, Matrix, cluster, MASS, pbmcapply,
optimx, methods
Kosuke Hamazaki [aut, cre],
Hiroyoshi Iwata [aut, ctb]

By using 'RAINBOWR' (Reliable Association INference By Optimizing Weights with R), users can test multiple SNPs (Single Nucleotide Polymorphisms) simultaneously by kernel-based (SNP-set) methods. This package can also be applied to haplotype-based GWAS (Genome-Wide Association Study). Users can test not only additive effects but also dominance and epistatic effects. In detail, please check our paper on PLOS Computational Biology: Kosuke Hamazaki and Hiroyoshi Iwata (2020) <doi:10.1371/journal.pcbi.1007663>.
Rcpp, rrBLUP, rgl, tcltk, Matrix, cluster, MASS, pbmcapply,
optimx, methods, ape

Rcpp, rrBLUP, rgl, tcltk, Matrix, cluster, MASS, pbmcapply,
optimx, methods, ape, stringr

Rcpp, rgl, tcltk, Matrix, cluster, MASS, pbmcapply, optimx,
methods, ape, stringr, pegas, ggplot2, ggtree, scatterpie,
phylobase, haplotypes, ggimage, rrBLUP, expm, parallel, pbapply

Rcpp, Matrix, cluster, MASS, pbmcapply, optimx, methods, ape,
stringr, pegas, ggplot2, ggtree, scatterpie, phylobase,
haplotypes, rrBLUP, expm, here, htmlwidgets, Rfast

Rcpp, Matrix, cluster, MASS, pbmcapply, optimx, methods, ape,
stringr, pegas, rrBLUP, expm, here, htmlwidgets, Rfast, gaston,
MM4LMM
knitr, rmarkdown, plotly, haplotypes, adegenet, ggplot2,
ggtree, scatterpie, phylobase, furrr, future, progressr,
foreach, doParallel