1 Installation

To install the hespresso package, start R and run the following commands:

# CRAN Packages
install.packages(c("remotes", "BiocManager"))

# edgeR for dispersion estimation
BiocManager::install("edgeR")

# cmdstanr for MCMC sampling
install.packages("cmdstanr", repos = c("https://stan-dev.r-universe.dev", getOption("repos")))
cmdstanr::install_cmdstan()

# hespresso
remotes::install_github("bitdessin/hespresso")

Because hespresso relies on cmdstanr (Gabry et al. 2025), which is not available on CRAN or Bioconductor, it cannot be hosted on these repositories, making the installation slightly more complex than that of typical R packages.