• GCTA

  • Referenced in 16 articles [sw23135]
  • SNPs identified by genome-wide association studies (GWAS) explain only a small fraction ... estimation of the linkage disequilibrium structure, and GWAS simulation. We focus on the function ... partition complex trait variation with large GWAS data sets...
  • MaCH

  • Referenced in 7 articles [sw17274]
  • unobserved genotypes. Genome-wide association studies (GWAS) can identify common alleles that contribute to complex ... studies as well as meta-analyses of GWAS. Here, we use simulations and experimental genotypes...
  • SNPinfo

  • Referenced in 3 articles [sw17360]
  • SNPinfo: integrating gwas and candidate gene information into functional SNP selection for genetic association studies ... linkage regions and select SNPs based on GWAS results, linkage disequilibrium (LD), and predicted functional ... coding SNPs. The algorithm uses GWAS SNP P-value data and finds all SNPs ... high LD with GWAS SNPs, so that selection is from a much larger...
  • dmGWAS

  • Referenced in 3 articles [sw29291]
  • recent success of genome-wide association studies (GWAS) is how to detect genetic signals beyond ... complex diseases and traits. Integrative testing of GWAS association data with that from prior-knowledge ... diseases by integrating the association signal from GWAS datasets into the human protein-protein interaction ... enriched with low P-value genes in GWAS datasets. Compared with pathway-based approaches, this...
  • ToppGene Suite

  • Referenced in 6 articles [sw30169]
  • ToppGene Suite using 20 recently reported GWAS-based gene–disease associations (including novel disease genes...
  • TATES

  • Referenced in 3 articles [sw20044]
  • date, the genome-wide association study (GWAS) is the primary tool to identify genetic variants ... that cause phenotypic variation. As GWAS analyses are generally univariate in nature, multivariate phenotypic information ... combines p-values obtained in standard univariate GWAS to acquire one trait-based p-value...
  • GEMMA

  • Referenced in 4 articles [sw23999]
  • close relatives for genome-wide association studies (GWAS): It fits a univariate linear mixed model...
  • RSS

  • Referenced in 2 articles [sw23316]
  • analysis of genome-wide association studies (GWAS). For example, they can estimate heritability of complex ... detecting associations. We apply RSS to a GWAS of human height that contains...
  • GBOOST

  • Referenced in 2 articles [sw25801]
  • 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...
  • MixMAP

  • Referenced in 2 articles [sw35575]
  • association using data from a previous GWAS or data from a meta-analysis of several ... GWAS. Conceptually, genes are detected as significant if the collection of p-values within...
  • EPIQ

  • Referenced in 1 article [sw26695]
  • Unlike single-locus genome-wide association studies (GWAS), which proved efficient in detecting numerous genetic ... loci related with various traits, interaction-based GWAS have so far produced very few reproducible ... efficient algorithm for detecting epistasis in quantitative GWAS, achieving a substantial runtime speedup by avoiding ... tool named EPIQ (EPIstasis detection for Quantitative GWAS), and we show by simulations that EPIQ...
  • r2VIM

  • Referenced in 1 article [sw27009]
  • analyses in genome-wide association studies (GWAS). RFs provide variable importance measures (VIMs) to rank ... selected as important. Evaluations on simulated GWAS data show that the new method controls ... powerful than logistic regression. In an experimental GWAS data set, the same strong signal ... when using linear regression. In another underpowered GWAS data set, the approach selects none...
  • XPEB

  • Referenced in 1 article [sw33849]
  • input P-value summary statistics from two GWAS, a target-GWAS from for example ... primary interest and an auxiliary base-GWAS such as a larger GWAS in Europeans...
  • PERMORY

  • Referenced in 1 article [sw35193]
  • testing. Motivation: In genome-wide association studies (GWAS) examining hundreds of thousands of genetic markers ... gold standard for multiple testing correction in GWAS, because they simultaneously provide unbiased type ... especially with large-scale datasets of modern GWAS. In recent years, the computational problem ... original computational problem of permutation testing in GWAS and herein present a permutation test algorithm...
  • CAPL

  • Referenced in 1 article [sw18853]
  • Background: With many genome-wide association study (GWAS) datasets available, it is critical that ... implementation of CAPL can analyze a large GWAS dataset in a reasonable time frame when ... computing resource is available. Conclusions: As many GWAS datasets based on both family and case...
  • GLOGS

  • Referenced in 1 article [sw23133]
  • GLOGS: a fast and powerful method for GWAS of binary traits with risk covariates ... based approaches to genome-wide association studies (GWAS) of binary traits in related individuals ... covariate effects increase, and can complete a GWAS in minutes. Availability: Source code and documentation...
  • genMOSS

  • Referenced in 2 articles [sw17049]
  • gennMOSS: Functions for the Bayesian Analysis of GWAS Data. Implements the Mode Oriented Stochastic Search...
  • CNVassoc

  • Referenced in 2 articles [sw19389]
  • analyses of Genome Wide Association studies (GWAs) with hundreds of thousands of genetic variants (CNVs...
  • Postgwas

  • Referenced in 2 articles [sw23137]
  • contains an interaction network analysis tool for GWAS result data. Special features cover subphenotype (intermediate...
  • GWASpi

  • Referenced in 2 articles [sw30109]
  • Studies pipeline. A (Java) tool (GUI & scriptable) GWAS on the desktop. A tool to perform...