R (>= 2.10), gridExtra, ggplot2, partykit, Rcpp

Efficient Mixed Model Analysis of Count Data in Large-Scale
Genomic Sequencing Studies
An efficient tool designed for differential analysis of large-scale RNA sequencing (RNAseq) data and Bisulfite sequencing (BSseq) data in the presence of individual relatedness and population structure. 'PQLseq' first fits a Generalized Linear Mixed Model (GLMM) with adjusted covariates, predictor of interest and random effects to account for population structure and individual relatedness, and then performs Wald tests for each gene in RNAseq or site in BSseq.

Conduct a Prospective or Retrospective Design Analysis
c(person(given = "Claudio",
family = "Zandonella Callegher",
role = c("aut", "cre"),
email = "claudiozandonella@gmail.com",
comment = c(ORCID = "0000-0001-7721-6318")),
person(given = "Massimiliano",
family = "Pastore",
role = "aut",
email = "massimiliano.pastore@unipd.it",
comment = c(ORCID = "0000-0002-7922-6365")),
person(given = "Angela",
family = "Andreella",
role = "aut",
email = "a.andreella8@gmail.com",
comment = c(ORCID = "0000-0002-1141-3041")),
person(given = "Anna",
family = "Vesely",
role = "aut",
email = "anna.vesely92@gmail.com",
comment = c(ORCID = "0000-0001-6696-2390")),
person(given = "Enrico",
family = "Toffalini",
role = "aut",
email = "enrico.toffalini@yahoo.it",
comment = c(ORCID = "0000-0002-1404-5133")),
person(given = "Giulia",
family = "Bertoldo",
role = "aut",
email = "giuliabertoldo94@gmail.com",
comment = c(ORCID = "0000-0002-6960-3980")),
person(given = "Gianmarco",
family = "Altoè",
role = "aut",
email = "gianmarco.altoe@unipd.it",
comment = c(ORCID = "0000-0003-1154-9528")))
An implementation of the "Design Analysis" proposed by
Gelman and Carlin (2014) <doi:10.1177/1745691614551642>. It combines
the evaluation of Power-Analysis with other inferential-risks as
Type-M error (i.e. Magnitude) and Type-S error (i.e. Sign). See also
Altoè et al. (2020) <doi:10.3389/fpsyg.2019.02893> and
Bertoldo et al. (2020) <doi:10.31234/osf.io/q9f86>.
covr, devtools, ggplot2, knitr, rmarkdown, roxygen2,
testthat, tidyverse
Claudio Zandonella Callegher [aut, cre]
(<https://orcid.org/0000-0001-7721-6318>),
Massimiliano Pastore [aut] (<https://orcid.org/0000-0002-7922-6365>),
Angela Andreella [aut] (<https://orcid.org/0000-0002-1141-3041>),
Anna Vesely [aut] (<https://orcid.org/0000-0001-6696-2390>),
Enrico Toffalini [aut] (<https://orcid.org/0000-0002-1404-5133>),
Giulia Bertoldo [aut] (<https://orcid.org/0000-0002-6960-3980>),
Gianmarco Altoè [aut] (<https://orcid.org/0000-0003-1154-9528>)