gene_color

This function merges selected genes with differential expression data and adds a color column based on up/down regulation.

A tool for comprehensive transcriptomic data analysis, with a focus on transcript-level data preprocessing, expression profiling, differential expression analysis, and functional enrichment. It enables researchers to identify key biological processes, disease biomarkers, and gene regulatory mechanisms. 'TransProR' is aimed at researchers and bioinformaticians working with RNA-Seq data, providing an intuitive framework for in-depth analysis and visualization of transcriptomic datasets. The package includes comprehensive documentation and usage examples to guide users through the entire analysis pipeline. The differential expression analysis methods incorporated in the package include 'limma' (Ritchie et al., 2015, <doi:10.1093/nar/gkv007>; Smyth, 2005, <doi:10.1007/0-387-29362-0_23>), 'edgeR' (Robinson et al., 2010, <doi:10.1093/bioinformatics/btp616>), 'DESeq2' (Love et al., 2014, <doi:10.1186/s13059-014-0550-8>), and Wilcoxon tests (Li et al., 2022, <doi:10.1186/s13059-022-02648-4>), providing flexible and robust approaches to RNA-Seq data analysis. For more information, refer to the package vignettes and related publications.

Dongyue Yu

TransProR

Analysis and Visualization of Multi-Omics Data

gene_color function

<dl><dt>selected_genes</dt>
<dd>A data frame containing selected genes with a column named "Symble".</dd>
<dt>DEG_deseq2</dt>
<dd>A data frame containing differential expression data with a column named "Symble" and a column named "change" indicating up/down regulation.</dd>
<dt>up_color</dt>
<dd>The color to assign to genes with up-regulated expression.</dd>
<dt>down_color</dt>
<dd>The color to assign to genes with down-regulated expression.</dd></dl>

Arguments

Merge Genes with Color Information Based on Up/Down Regulation — gene_color

<dl>

<dt>selected_genes</dt>
<dd>A data frame containing selected genes with a column named "Symble".</dd>


<dt>DEG_deseq2</dt>
<dd>A data frame containing differential expression data with a column named "Symble" and a column named "change" indicating up/down regulation.</dd>


<dt>up_color</dt>
<dd>The color to assign to genes with up-regulated expression.</dd>


<dt>down_color</dt>
<dd>The color to assign to genes with down-regulated expression.</dd>

</dl>

gene_color: Merge Genes with Color Information Based on Up/Down Regulation

Description

Usage

Value

Arguments

Examples