download_gene_ref

Downloads a standardized gene annotation table for human or mouse using <code>biomaRt</code>.
Includes Ensembl ID, gene symbol, Entrez ID, gene type, chromosome location, and other metadata.

A comprehensive collection of utility functions for data analysis
and visualization in R. The package provides 60+ functions for data
manipulation, file handling, color palette management, bioinformatics
workflows, statistical analysis, plotting, and package management. Features include void value
handling, custom infix operators, flexible file I/O, and publication-ready
visualizations with sensible defaults. Implementation follows tidyverse
principles (Wickham et al. (2019) <doi:10.21105/joss.01686>) and incorporates
best practices from the R community.

Evan Zhou

evanverse

Utility Functions for Data Analysis and Visualization

download_gene_ref function

<dl><dt>species</dt>
<dd>Organism, either <code>"human"</code> or <code>"mouse"</code>. Default is <code>"human"</code>.</dd>
<dt>remove_empty_symbol</dt>
<dd>Logical. Remove entries with missing gene symbol. Default: <code>FALSE</code>.</dd>
<dt>remove_na_entrez</dt>
<dd>Logical. Remove entries with missing Entrez ID. Default: <code>FALSE</code>.</dd>
<dt>save</dt>
<dd>Logical. Whether to save the result as <code>.rds</code>. Default: <code>FALSE</code>.</dd>
<dt>save_path</dt>
<dd>File path to save (optional). If <code>NULL</code>, will use default <code>gene_ref_&lt;species&gt;_&lt;date&gt;.rds</code>.</dd></dl>

Arguments

Download gene annotation reference table from Ensembl — download_gene_ref

<dl>

<dt>species</dt>
<dd>Organism, either <code>"human"</code> or <code>"mouse"</code>. Default is <code>"human"</code>.</dd>


<dt>remove_empty_symbol</dt>
<dd>Logical. Remove entries with missing gene symbol. Default: <code>FALSE</code>.</dd>


<dt>remove_na_entrez</dt>
<dd>Logical. Remove entries with missing Entrez ID. Default: <code>FALSE</code>.</dd>


<dt>save</dt>
<dd>Logical. Whether to save the result as <code>.rds</code>. Default: <code>FALSE</code>.</dd>


<dt>save_path</dt>
<dd>File path to save (optional). If <code>NULL</code>, will use default <code>gene_ref_&lt;species&gt;_&lt;date&gt;.rds</code>.</dd>

</dl>

download_gene_ref: Download gene annotation reference table from Ensembl

Description

Usage

Value

Arguments