## ----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()