read_gmt

Assignment of cell type labels to single-cell RNA sequencing (scRNA-seq) clusters is often a time-consuming process that involves manual inspection of the cluster marker genes complemented with a detailed literature search. This is especially challenging when unexpected or poorly described populations are present. The clustermole R package provides methods to query thousands of human and mouse cell identity markers sourced from a variety of databases.

Igor Dolgalev

clustermole

Unbiased Single-Cell Transcriptomic Data Cell Type
Identification

read_gmt function

<dl><dt>file</dt>
<dd>A connection object or a character string (can be a URL).</dd>
<dt>geneset_label</dt>
<dd>Column name for gene sets (first column of the GMT file) in the output data frame.</dd>
<dt>gene_label</dt>
<dd>Column name for genes (variable columns of the GMT file) in the output data frame.</dd></dl>

Arguments

Read a GMT file into a data frame — read_gmt

<dl>

<dt>file</dt>
<dd>A connection object or a character string (can be a URL).</dd>


<dt>geneset_label</dt>
<dd>Column name for gene sets (first column of the GMT file) in the output data frame.</dd>


<dt>gene_label</dt>
<dd>Column name for genes (variable columns of the GMT file) in the output data frame.</dd>

</dl>

read_gmt: Read a GMT file into a data frame

Description

Usage

Value

Arguments

Examples