## ----setup, include = FALSE, echo=FALSE, results="hide", message=FALSE--------
require(knitr)

knitr::opts_chunk$set(
    collapse = TRUE,
    comment = "#>",
    error = FALSE,
    warning = FALSE,
    message = FALSE,
    crop = NULL
)
stopifnot(requireNamespace("htmltools"))
htmltools::tagList(rmarkdown::html_dependency_font_awesome())


## ----library------------------------------------------------------------------
library(orthosData)

## ----eval=F, echo=T-----------------------------------------------------------
#  # Check the path to the user's ExperimentHub directory:
#  ExperimentHub::getExperimentHubOption("CACHE")
#  # Download and cache the models for a specific organism:
#  GetorthosModels(organism = "Mouse")
#  

## ----eval=F, echo=T-----------------------------------------------------------
#  # Check the path to the user's ExperimentHub directory:
#  ExperimentHub::getExperimentHubOption("CACHE")
#  
#  # Download and cache the contrast database for a specific organism.
#  # Note: mode="DEMO" caches a small "toy" database for the queries for demonstration purposes
#  # To download the full db use mode = "ANALYSIS" (this is time and space consuming)
#  GetorthosContrastDB(organism = "Mouse", mode="DEMO")
#  
#  # Load the HDF5SummarizedExperiment:
#  se <- HDF5Array::loadHDF5SummarizedExperiment(dir = ExperimentHub::getExperimentHubOption("CACHE"),
#  prefix = "mouse_v212_NDF_c100_DEMO")

## -----------------------------------------------------------------------------
sessionInfo()