Powerful Replicability Analysis of Genome-Wide Association Studies R package ReAD version 1.0.1 A robust and powerful approach is developed for replicability analysis of two Genome-wide association studies (GWASs) accounting for the linkage disequilibrium (LD) among genetic variants. The LD structure in two GWASs is captured by a four-state hidden Markov model (HMM). The unknowns involved in the HMM are estimated by an efficient expectation-maximization (EM) algorithm in combination with a non-parametric estimation of functions. By incorporating information from adjacent locations via the HMM, this approach identifies the entire clusters of genotype-phenotype associated signals, improving the power of replicability analysis while effectively controlling the false discovery rate. Software Depends: Rcpp (>= 1.0.10), qvalue LinkingTo: Rcpp, RcppArmadillo Yan Li <yanli_@jlu.edu.cn> Comprehensive R Archive Network (CRAN) Yan Li [aut, cre, cph], Haochen lei [aut], Xiaoquan Wen [aut], Hongyuan Cao [aut] GPL-3 2023-06-30 application/tgz https://CRAN.R-project.org/package=ReAD doi:10.32614/CRAN.package.ReAD