## ----include = FALSE----------------------------------------------------------
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

## ----echo=FALSE, out.width="100%", fig.align="center"-------------------------
knitr::include_graphics("figures/20250925_graphical_abstract_rChEA3_v1.png")

## ----install-stable, eval=FALSE-----------------------------------------------
# install.packages("rChEA3")

## ----install-dvpt, eval=FALSE-------------------------------------------------
# # install.packages("pak")  # if not already installed
# pak::pak("ckntav/rChEA3")
# 
# # or, alternatively:
# # install.packages("devtools")  # if not already installed
# devtools::install_github("ckntav/rChEA3")

## ----setup--------------------------------------------------------------------
library(rChEA3)

## ----submit-------------------------------------------------------------------
genes <- c("TP53", "ESR1", "MYC", "NIPBL", "BRCA1")
results <- queryChEA3(genes)

## ----submit_local, eval=FALSE-------------------------------------------------
# results <- queryChEA3(genes, url = "http://localhost:8080/chea3/api/enrich/")

## ----inspect------------------------------------------------------------------
displayTopN(results)

## ----extract------------------------------------------------------------------
meanRank_results <- results[["Integrated--meanRank"]]
head(meanRank_results)

## ----visualize----------------------------------------------------------------
visualizeRank(meanRank_results)

## ----session-info-------------------------------------------------------------
sessionInfo()