Data

Tools

Indexes

Applications

Experiments

Open Source Science

https://github.com/arunbodd/vcp_nulisa-seq_rshiny

https://github.com/arunbodd/vcp_nulisa-seq_rshiny

Science Score: 13.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ○
    .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ○
    Committers with academic emails
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (13.0%) to scientific vocabulary
Last synced: 10 months ago · JSON representation

Repository

Basic Info
  • Host: GitHub
  • Owner: arunbodd
  • License: mit
  • Language: R
  • Default Branch: main
  • Size: 66.4 KB
Statistics
  • Stars: 0
  • Watchers: 1
  • Forks: 0
  • Open Issues: 0
  • Releases: 0
Created about 1 year ago · Last pushed about 1 year ago
Metadata Files
Readme License

README.md

VCF vs Control Proteomics Analysis

A Shiny application for analyzing proteomics data comparing VCF and Control samples.

Features

  • Dataset Overview: View sample information and basic statistics
  • PCA Analysis: Interactive PCA plot with customizable options
  • Differential Expression Analysis: Volcano plot and table of differentially expressed proteins
  • Heatmap Visualization: Customizable heatmap of top differentially expressed proteins
  • ROC Analysis: Single and multi-protein ROC curve analysis with LOOCV
  • Protein Visualization: Boxplots, violin plots, and line plots for individual proteins

Requirements

The application requires the following R packages:

r library(shiny) library(shinydashboard) library(dplyr) library(ggplot2) library(DT) library(pROC) library(reshape2) library(plotly) library(ggrepel) library(stringr) library(tidyr) library(pheatmap) library(RColorBrewer) library(ComplexHeatmap) library(circlize) library(STRINGdb) library(igraph) library(ggpubr) library(ggthemes) library(data.table) library(corrplot)

Running the Application

To run the application locally:

  1. Clone this repository: bash git clone https://github.com/arunbodd/VCF_NULISA-Seq_Rshiny.git cd VCF_NULISA-Seq_Rshiny

  2. Ensure your data files are in the data/ directory:

    • data/Controlonly_samples.csv: Control sample data
    • data/VCP_samples.csv: VCF sample data
    • data/Control_VCP_metadata.csv: Sample metadata

  3. Run the app: r shiny::runApp()

Live Demo

A live demo of the application is available at:

VCF vs Control Proteomics Analysis App

Data Format Requirements

  1. Control Samples CSV:

    • Must include columns: Control.Plasma, Target, and NPQ

  2. VCF Samples CSV:

    • Must include columns: VCP.Plasma, Target, and NPQ
    • Note: The file is still named VCP_samples.csv but the app refers to this as VCF

  3. Metadata CSV:

    • Must include a Sample column that matches the sample names in the data files

Deployment

If you wish to deploy your own version of this app:

  1. Install the rsconnect package: r install.packages("rsconnect")

  2. Set up your shinyapps.io account credentials using one of these secure methods:

Method A: Interactive setup (recommended for personal use) r # Run this in the R console, NOT in a script that will be committed to version control rsconnect::setAccountInfo( name='YOUR_ACCOUNT_NAME', token='YOUR_TOKEN', secret='YOUR_SECRET' )

Method B: Environment variables (recommended for teams/CI) r # Add to your .Renviron file (never commit this file to git) SHINYAPPS_NAME="YOUR_ACCOUNT_NAME" SHINYAPPS_TOKEN="YOUR_TOKEN" SHINYAPPS_SECRET="YOUR_SECRET"

  1. Use the provided deployment script: r source("deploy_app.R")

This will deploy the app with the data from your data/ directory.

Security Best Practices

  • NEVER commit API keys or secrets to version control
  • Use environment variables or interactive setup for credentials
  • Consider using .gitignore to exclude any files containing sensitive information
  • For team deployments, use CI/CD secrets management

Download Options

The application provides download options for all plots in various formats: - PNG - PDF - TIFF - JPEG

Future Development

There are plans to convert this application to Python using Streamlit for better user experience and visualization capabilities.

Owner

  • Name: Arun boddapati
  • Login: arunbodd
  • Kind: user
  • Location: Reston
  • Company: Leidos

GitHub Events

Total
  • Push event: 1
  • Create event: 1
Last Year
  • Push event: 1
  • Create event: 1

Committers

Last synced: about 1 year ago

All Time
  • Total Commits: 13
  • Total Committers: 1
  • Avg Commits per committer: 13.0
  • Development Distribution Score (DDS): 0.0
Past Year
  • Commits: 13
  • Committers: 1
  • Avg Commits per committer: 13.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
arunbodd a****d@o****m 13

Issues and Pull Requests

Last synced: about 1 year ago

All Time
  • Total issues: 0
  • Total pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Total issue authors: 0
  • Total pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
Pull Request Authors
Top Labels
Issue Labels
Pull Request Labels