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

## ----setup--------------------------------------------------------------------
library(scATAC.Explorer)

## -----------------------------------------------------------------------------
res = queryATAC(metadata_only = TRUE)

## ---- echo=FALSE--------------------------------------------------------------
knitr::kable(head(res[[1]][,1:5]))

## -----------------------------------------------------------------------------
res = queryATAC(disease = 'leukemia', metadata_only = TRUE)[[1]]

## ---- echo=FALSE--------------------------------------------------------------
knitr::kable(head(res[,1:5]))

## -----------------------------------------------------------------------------
res = queryATAC(accession = "GSE89362")

## ---- eval=FALSE--------------------------------------------------------------
#  View(counts(res[[1]]))

## ---- echo=FALSE--------------------------------------------------------------
knitr::kable(data.frame(as.matrix(counts(res[[1]][1:10,1:8]))))

## -----------------------------------------------------------------------------
metadata(res[[1]])$pmid

## ---- eval=FALSE--------------------------------------------------------------
#  res = queryATAC(has_cell_type = TRUE)

## ---- eval=FALSE--------------------------------------------------------------
#  View(colData(res[[1]]))

## ---- echo=FALSE--------------------------------------------------------------
knitr::kable(head(colData(res[[1]])))

## ---- eval=FALSE--------------------------------------------------------------
#  res = queryATAC(accession = "GSE89362")[[1]]
#  saveATAC(res, '~/Downloads/GSE89362')

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