'XZDBfunction' R Package

• A user-friendly website browser application for searching, annotating, and exporting genomic and proteomic metadata across multiple datasets.
• Only dependency is R (Shiny UI), work for Windows, Mac, and linux.
• Easy lunch script available (both Windows and MacOS system).
• Also contains daily analysis functions for statistics and biology.

This document provides complete instructions for starting the website browser application and its functions.

Quick tour (R)

install.packages("remotes")
remotes::install_github("scottcalcalas/XZDBfunction")
library(XZDBfunction)
XZDB.Run() #Run a demo - with example datasets

Use

Installation at R

install.packages("remotes") # Skip this step if you already have "remotes" package

remotes::install_github("scottcalcalas/XZDBfunction")

library(XZDBfunction)

Get protocol and Set up your own database

?xzdb.help()
xzdb.help() #Get protocols and setup instructions

#transfer your datasets to current folder, check everything ok to run next step.
xiaopei.input.all()    #Build database in current folder and copy them to R package.
#After this step, R always use your own dataset instead of example dataset

Use Genomic website browser

XZDB.Run()                 # lunches browser, if you already finished running xiaopei.input.all(), it will use your own dataset instead of example dataset

XZDB.Run(use_current = T)  # Required setup datasets to current path to search

---

Functions Contents

• 1. Print/Export
• 2. Check
• 3. Load Index File
• 4. Output Files
• 5. Update Database
• 6. UniProt / MINT Comparison
• Browser Files: Add Your Own Dataset & Dataset Information

Function 1 — Print/Export

Use the Print/Export tab to obtain detailed search results.

Supported search options:

• Gene Symbol — exact, family, fuzzy
• Protein ID — exact match
• ENSEMBL Gene ID — exact match

Example: searching CDK13 and NCBP2 returns all matching rows across all datasets.

The app generates three files automatically:

• Full results
• Details for Gene 1
• Details for Gene 2

Function 2 — Check

Use the Check tab to:

• See which datasets include a specific gene
• Quickly confirm if the gene exists in the database

Function 3 — Load Index File

On the left panel, use Load Data info to view dataset metadata and structure.

Function 4 — Output Files

Open the Output files tab to:

• Preview a result file (using the red Preview Selected button)
• Download results (using the Download button in each row)

Note:
Not all outputs can be previewed.
The output folder may be cleared monthly—please save results you want to keep.

Function 5 — Update Database

(Optional — only needed if updating dataset metadata)

After updating:

• datasets/
• Datasets infomation.xlsx

Run "Rebuild EVERYTHING" at Administrator Operations in the left panel:

Function 6 — UniProt / MINT Comparison

• UniProt: retrieves protein entry information
• MINT: retrieves protein–protein interaction data based on UniProt ID

Requires an internet connection.

Browser files

To use your own dataset and dataset information(saving to package storage or run on current path), use:

xiaopei.input.all()

Use helper to create your own dataset, run:

xzdb.help()
xiaopei.input.all()    # Run this after modified copied files

Example package storage location, inside R package:

 R\R-4.4.3\library\XZDBfunction\shinyapp

You can find Datasets infomation.xlsx ; For putting dataset, goes to dataset folder After done those, start broswer can run "Rebuild EVERYTHING" at Administrator Operations

---

Local use protocol

(If you want to use it as one click, instead of open R)

Author: Xiaopei
Updated: 2025-11-20

Contents

• 0. Configure R file
• 1. Auto Start
  • On Windows
  • On Mac
• 2.Start & Package Installation
• 3.Last Step
• Appendix — Windows & Mac Shortcuts

0. Configure R file

To make an quick start R file, put this two lines:

library(XZDBfunction)
XZDB.Run()

For example, it can be called Quick_Start.R. The next step is just setting up to run this file using R software(Not R-studio).

1. Auto Start

(Check examples at Appendix)

On Windows:

A desktop shortcut can automatically launch the Genomic DB Browser, as long as R is installed.

On Mac:

1. Ensure R is installed.
2. Open the project folder.
3. Double-click MAC_Start.command. If the Mac start script fails, use the backup version inside the App_Info folder.

2.Start & Package Installation

On the first run, the script will automatically install any missing R packages.

Once installation finishes, the app will open in your browser automatically.

3.Last Step

After finishing:

• Close the browser tab
• Close R / RStudio / Terminal

Appendix

A1.Windows Shortcut Example

Modify the shortcut Target to point to Rscript and your Quick Start script: (For example:)

C:\Users\jcc1885\AppData\Local\Programs\R\R-4.4.3\bin\Rscript.exe "R:\Basic_Sciences\Pharm\Borden_Lab\borden\Database\Genomic result Browser\Quick Start.R"

A2.Mac “One-Click Start” Command File

Create a file named something.command (e.g. MAC_Start.command) on the Desktop:

#!/bin/bash
# Launch script
# ...

Then run

cd ~/Desktop
chmod +x something.command

After those steps, Double-click the file can luanch the website browser application.

A3. Update local R script (For Borden Lab at Northwestern University)

Copy and replace your local scripts using the scripts at github location: XZDBfunction/inst/shinyapp/