Parallel Computing Toolset for Genome-Wide Association Studies
(GWAS)
A High-performance computing toolset for relatedness and
principal component analysis of SNP data

A High-performance computing toolset for relatedness and principal component analysis of SNP data

A high-performance computing toolset for relatedness and
principal component analysis in GWAS

Investigating the Functional Characteristics of Selected SNPs
and Their Vicinity Genomic Region
c(
person(given = "Alireza", family = "Ani", role = c("aut", "cre"), email = "a.ani@umcg.nl"),
person(given = "Zoha", family = "Kamali", role = "aut"),
person(given = "Ahmad", family = "Vaez", role = "aut"))
Alireza Ani [aut, cre],
Zoha Kamali [aut],
Ahmad Vaez [aut]
data.table, httr, jsonlite, xml2, openxlsx, progress,
doParallel, foreach, ggplot2, kableExtra, methods, rmarkdown
To investigate the functional characteristics of selected SNPs and their vicinity genomic region. Linked SNPs in moderate to high linkage disequilibrium (e.g. r2>0.50) with the corresponding index SNPs will be selected for further analysis.

SNPs-based whole genome association studies
Juan R González, Lluís Armengol, Elisabet Guinó, Xavier Solé, and Víctor Moreno
This package carries out most common analysis when performing whole genome association studies. These analyses include descriptive statistics and exploratory analysis of missing values, calculation of Hardy-Weinberg equilibrium, analysis of association based on generalized linear models (either for quantitative or binary traits), and analysis of multiple SNPs (haplotype and epistasis analysis)

This package carries out most common analysis when performing whole genome association studies. These analyses include descriptive statistics and exploratory analysis of missing values, calculation of Hardy-Weinberg equilibrium, analysis of association based on generalized linear models (either for quantitative or binary traits), and analysis of multiple SNPs (haplotype and epistasis analysis). Permutation test and related tests (sum statistic and truncated product) are also implemented.