• GCTA

  • Referenced in 22 articles [sw23135]
  • SNPs identified by genome-wide association studies (GWAS) explain only a small fraction ... user-friendly software tool called genome-wide complex trait analysis (GCTA), which was developed based ... whole genome for a complex trait rather than testing the association of any particular ... introduce GCTA’s five main functions: data management, estimation of the genetic relationships from...
  • MaCH

  • Referenced in 7 articles [sw17274]
  • genotype data to estimate haplotypes and unobserved genotypes. Genome-wide association studies (GWAS ... uses available genotype and shotgun sequence data to estimate unobserved genotypes and haplotypes, together ... these estimates. Our approach is already widely used to facilitate comparison of results across studies ... very accurate using either genome-wide SNP data or smaller amounts of data...
  • GWAS Catalog

  • Referenced in 15 articles [sw41505]
  • number of published genome-wide association studies (GWAS). These studies provide an unprecedented opportunity ... identifying published GWAS can be challenging, and the vast wealth of data contained within...
  • RVFam

  • Referenced in 0 articles [sw18961]
  • RVFam (Rare Variant association analysis with Family data) designed to analyze continuous, binary ... sequencing variants in genome-wide association studies (GWAS) involving family data. Single and multiple...
  • CAPL

  • Referenced in 1 article [sw18853]
  • data and accounting for population stratification. Background: With many genome-wide association study (GWAS ... account for population stratification in the data. Because computationally intensive algorithms are used...
  • RSS

  • Referenced in 2 articles [sw23316]
  • approaches to the analysis of genome-wide association studies (GWAS). For example, they can estimate ... sparse models; and by incorporating external genomic data into the priors, they can increase...
  • GEMMA

  • Referenced in 5 articles [sw23999]
  • close relatives for genome-wide association studies (GWAS): It fits a univariate linear mixed model ... marker association tests with a single phenotype to account for population stratification and sample structure ... linear mixed model (mvLMM) for testing marker associations with multiple phenotypes simultaneously while controlling ... typed genotypes, predicting phenotypes, and identifying associated markers by jointly modeling all markers while controlling...
  • HEALER

  • Referenced in 1 article [sw30527]
  • Motivation: Genome-wide association studies (GWAS) have been widely used in discovering the association between ... genotypes and phenotypes. Human genome data contain valuable but highly sensitive information. Unprotected disclosure...
  • dmGWAS

  • Referenced in 3 articles [sw29291]
  • from the recent success of genome-wide association studies (GWAS) is how to detect genetic ... traits. Integrative testing of GWAS association data with that from prior-knowledge databases...
  • GBOOST

  • Referenced in 2 articles [sw25801]
  • With a huge amount of genetic variations data in hand, developing efficient algorithms ... problems in genome-wide association studies (GWAS). Boolean operation-based screening and testing (BOOST ... recent work in GWAS, completes gene-gene interaction analysis in 2.5 days on a desktop ... Consortium Type 2 Diabetes (WTCCC T2D) genome data within 1.34 h on a desktop...
  • geneSLOPE

  • Referenced in 0 articles [sw17390]
  • package geneSLOPE. Genome-wide association study (GWAS) performed with SLOPE, short for Sorted ... linear model. In the first step of GWAS, SNPs are clumped according to their correlations ... distances. Then, SLOPE is performed on data where each clump has one representative...
  • BlueSNP

  • Referenced in 1 article [sw12005]
  • Hadoop clusters. Computational workloads for genome-wide association studies (GWAS) are growing in scale ... personal computers. The BlueSNP R package implements GWAS statistical tests in the R programming language ... facto standard framework for distributed data processing using the MapReduce formalism. BlueSNP makes computationally...
  • r2VIM

  • Referenced in 1 article [sw27009]
  • standard single SNP analyses in genome-wide association studies (GWAS). RFs provide variable importance measures ... selected as important. Evaluations on simulated GWAS data show that the new method controls...
  • GWAPP

  • Referenced in 1 article [sw29292]
  • organism for understanding natural variation. Genome-wide association studies (GWAS) have proven a useful technique ... different traits. These important features greatly simplify association mapping of traits and allow for systematic ... interactive Web-based application for conducting GWAS in A. thaliana. Using an efficient implementation ... disequilibrium plots. It also facilitates exploratory data analysis by implementing features such...
  • EPIQ

  • Referenced in 1 article [sw26695]
  • other organisms. Unlike single-locus genome-wide association studies (GWAS), which proved efficient in detecting ... loci related with various traits, interaction-based GWAS have so far produced very few reproducible ... leading to reliable discoveries. For quantitative data, on the other hand, only a handful...
  • REMI

  • Referenced in 1 article [sw41504]
  • statistics. This problem is motivated by genome-wide association studies (GWASs) with millions of genotyped ... single nucleotide polymorphisms (SNPs), which have been widely used to identify risk variants among complex ... because of the inaccessibility of individual-level data. In this study, we propose ... highly scalable and capable of analyzing multiple GWAS data sets from hundreds of thousands...
  • GW-SEM

  • Referenced in 1 article [sw37731]
  • statistical methods used to analyze the data are relatively elementary and do not directly ... association of a SNP with multiple phenotypes or a latent construct on a genome-wide ... comparison with and existing multivariate GWAS software package...
  • R

  • Referenced in 9969 articles [sw00771]
  • R is a language and environment for statistical...
  • Bioconductor

  • Referenced in 319 articles [sw04205]
  • Bioconductor provides tools for the analysis and comprehension...
  • CRAN

  • Referenced in 552 articles [sw04351]
  • R is ‘GNU S’, a freely available language...