Query Composite Hypotheses R package qch version 2.1.3 Provides functions for the joint analysis of Q sets of p-values obtained for the same list of items. This joint analysis is performed by querying a composite hypothesis, i.e. an arbitrary complex combination of simple hypotheses, as described in Mary-Huard et al. (2021) <doi:10.1093/bioinformatics/btab592> and De Walsche et al.(2025) <doi: 10.1093/nargab/lqaf118>. In this approach, the Q-uplet of p-values associated with each item is distributed as a multivariate mixture, where each of the 2^Q components corresponds to a specific combination of simple hypotheses. The dependence between the p-value series is considered using a Gaussian copula function. A p-value for the composite hypothesis test is derived from the posterior probabilities. Software Depends: R (>= 2.10) Imports: copula, dplyr, graphics, ks, purrr, Rcpp, stats, stringr, utils LinkingTo: Rcpp, RcppArmadillo Tristan Mary-Huard <tristan.mary-huard@agroparistech.fr> Comprehensive R Archive Network (CRAN) Tristan Mary-Huard [aut, cre] (ORCID: <https://orcid.org/0000-0002-3839-9067>), Annaig De Walsche [aut] (ORCID: <https://orcid.org/0000-0003-0603-1716>), Franck Gauthier [ctb] (ORCID: <https://orcid.org/0000-0003-0574-065X>) GPL-3 2026-05-27 application/tgz https://CRAN.R-project.org/package=qch doi:10.32614/CRAN.package.qch