get_ucsc_reference: Build reference atlases from external UCSC cellbrowsers

In NCBI-Hackathons/clustifyR: Classifier for Single-cell RNA-seq Using Cell Clusters

Build reference atlases from external UCSC cellbrowsers

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

Value

reference matrix

Examples

## Not run: 

# 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
)

## End(Not run)

NCBI-Hackathons/clustifyR documentation built on Aug. 31, 2024, 5:35 a.m.