Build reference atlases from external UCSC cellbrowsers

Usage

get_ucsc_reference(cb_url, cluster_col, ...)

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

Value

reference matrix

Examples

if (FALSE) { # \dontrun{

# 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
)
} # }