This document provides complete instructions for starting the website browser application and its functions.
install.packages("remotes")
remotes::install_github("scottcalcalas/XZDBfunction")
library(XZDBfunction)
XZDB.Run() #Run a demo - with example datasets
install.packages("remotes") # Skip this step if you already have "remotes" package
remotes::install_github("scottcalcalas/XZDBfunction")
library(XZDBfunction)
?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
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 searchFunctions 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
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
Use the Check tab to: - See which datasets include a specific gene
- Quickly confirm if the gene exists in the database
On the left panel, use Load Data info to view dataset metadata and structure.
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.
To use your own dataset and dataset information(saving to package storage or run on current path), use:
Use helper to create your own dataset, run:
xzdb.help()
xiaopei.input.all() # Run this after modified copied filesExample package storage location, inside R package:
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
(If you want to use it as one click, instead of open R)
Author: Xiaopei
Updated: 2025-11-20
To make an quick start R file, put this two lines:
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).
(Check examples at Appendix)
On Windows:
A desktop shortcut can automatically launch the Genomic DB Browser, as long as R is installed.
On Mac:
App_Info folder.
On the first run, the script will automatically install any missing R packages.
Once installation finishes, the app will open in your browser automatically.
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"