/FragPipe-Analyst

Primary LanguageHTMLGNU General Public License v3.0GPL-3.0

Project Status: Active – The project has reached a stable, usable state and is being actively developed. R

FragPipe-Analyst

A tool for analyzing quantitative proteomics datasets for FragPipe.

Features

  • Differential expression analysis

  • Enrichment analysis (GO/Pathways)

  • Imputation (optional)

  • Data visualization

    1. PCA
    2. Sample correlation
    3. Heatmaps
    4. Missing value inspection
    5. Sample coverage
    6. Protein intensity plots for slected protein(s)
    7. Imputation effect evaluation
  • Report and multiple levels of exportable tables for further analysis

    • Table options
      • DE results
      • Unimputed data matrix: Original protein intensities before imputation
      • Imputed data matrix: Protein intensities after performing selected imputation method

Public servers

There are two server instances

Install on your own machine

Prerequisite

  • R 4.2
  • PDFlatex

Multiple options

Once all the dependencies are installed, follow steps below to run the server locally. You can build it natively:

# Clone the repository
git clone https://github.com/MonashProteomics/FragPipe-Analys.git

# Move to the folder
cd FragPipe-Analyst

# Inside R console or R studio
> library("shiny")
> runApp()

Or run it through Docker:

# Clone the repository
git clone https://github.com/MonashProteomics/FragPipe-Analys.git

# Move to the folder
cd FragPipe-Analyst

# Build FragPipe-Analyst (Any name after -t)
docker buildx build -f Dockerfile.local -t fragpipe-analyst  --output=type=docker --platform=linux/amd64 .

# Run FragPipe-Analyst
docker run -it --platform=linux/amd64 -d -p 3838:3838 fragpipe-analyst

# Open local interface
http://localhost:3838/fragpipe-analyst/