normalized_counts

Return a size-factor normalized and (optionally) log-transformed expression

Streamlining the clustering and visualization of time-series gene expression data from RNA-Seq experiments, this tool supports fuzzy c-means and k-means clustering algorithms. It is compatible with outputs from widely-used packages such as 'Seurat', 'Monocle', and 'WGCNA', enabling seamless downstream visualization and analysis. See Lokesh Kumar and Matthias E Futschik (2007) <doi:10.6026/97320630002005> for more details.

Junjun Lao

ClusterGVis

One-Step to Cluster and Visualize Gene Expression Data

Jun Zhang

normalized_counts function

<dl><dt>cds</dt>
<dd>A CDS object to calculate normalized expression matrix from.</dd>
<dt>norm_method</dt>
<dd>String indicating the normalization method. Options are
"log" (Default), "binary" and "size_only".</dd>
<dt>pseudocount</dt>
<dd>A pseudocount to add before log transformation. Ignored
if norm_method is not "log". Default is 1.</dd></dl>

Arguments

https://github.com/cole-trapnell-lab/monocle3
matrix

Author

Return a size-factor normalized and (optionally) log-transformed expression — normalized_counts

<dl>

<dt>cds</dt>
<dd>A CDS object to calculate normalized expression matrix from.</dd>


<dt>norm_method</dt>
<dd>String indicating the normalization method. Options are
"log" (Default), "binary" and "size_only".</dd>


<dt>pseudocount</dt>
<dd>A pseudocount to add before log transformation. Ignored
if norm_method is not "log". Default is 1.</dd>

</dl>

normalized_counts: Return a size-factor normalized and (optionally) log-transformed expression

Description

Usage

Value

Arguments

Author