generate_garnett_marker_file

Tibble of top markers, output of
<code><a rd-options="" href="/link/top_markers?package=monocle3&version=1.0.0" data-mini-rdoc="monocle3::top_markers">top_markers</a></code>.

marker_test_res

Path to the marker file to be generated. Default is
"./marker_file.txt".

file

Numeric, the maximum number of genes to output
per cell type entry. Default is 10.

max_genes_per_group

Logical indicating whether marker genes that
mark multiple cell groups should be excluded. Default is FALSE. When
FALSE, a message will be emitted when duplicates are present.

remove_duplicate_genes

Generate a Garnett marker file from top_markers output.

Monocle 3 performs clustering, differential expression and
trajectory analysis for single-cell expression experiments. It orders
individual cells according to progress through a biological process,
without knowing ahead of time which genes define progress through that
process. Monocle 3 also performs differential expression analysis,
clustering, visualization, and other useful tasks on single-cell expression
data.  It is designed to work with RNA-Seq data, but could be used with
other types as well.

Cole Trapnell

monocle3

Clustering, differential expression, and trajectory analysis for single-
cell RNA-Seq

generate_garnett_marker_file function

Tibble of top markers, output of
<code><a rd-options='' href='top_markers'>top_markers</a></code>.

generate_garnett_marker_file: Generate a Garnett marker file from top_markers output.

Description

Usage

Arguments

Value