get_ucsc_reference: Build reference atlases from external UCSC cellbrowsers

In clustifyr: Classifier for Single-cell RNA-seq Using Cell Clusters

Description

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

Examples

get_ext_reference(cb_url = "http://cells.ucsc.edu/?ds=kidney-atlas%2FFetal_Immune",
                 cluster_col = "celltype")

clustifyr documentation built on Nov. 8, 2020, 5:32 p.m.