Build reference atlases from external UCSC cellbrowsers
Source:R/cellbrowsers.R
get_ucsc_reference.Rd
Build reference atlases from external UCSC cellbrowsers
Arguments
- cb_url
URL of cellbrowser dataset (e.g. http://cells.ucsc.edu/?ds=cortex-dev). Note that the URL must contain the ds=dataset-name suffix.
- cluster_col
annotation field for summarizing gene expression (e.g. clustering, cell-type name, samples, etc.)
- ...
additional args passed to average_clusters
Examples
if (FALSE) {
# many datasets hosted by UCSC have UMI counts in the expression matrix
# set if_log = FALSE if the expression matrix has not been natural log transformed
get_ucsc_reference(cb_url = "https://cells.ucsc.edu/?ds=evocell+mus-musculus+marrow",
cluster_col = "Clusters", if_log = FALSE)
get_ucsc_reference(cb_url = "http://cells.ucsc.edu/?ds=muscle-cell-atlas",
cluster_col = "cell_annotation",
if_log = FALSE)
}