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

• Production server is hosted at https://fragpipe-analyst.org/.
• Dev server is also hosted at http://fragpipe-analyst.nesvilab.org/.

Documentation

Now documentation is all moved to here.

Install on your own machine

Two options are available right now for FragPipe-Analyst: local installation or run through Docker.

Local Installation

Prerequisite

• R >= 4.4
• PDFlatex

Once all the prerequisites are installed, follow steps below to build and run the server locally.

# 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
> install.packages("renv")
> renv::init(bioconductor = T)

# Install shiny.info, it's removed from CRAN since 2025-03-21 https://cran.r-project.org/web/packages/shiny.info/index.html, so we need to install their github version
> renv::install("Appsilon/shiny.info")

# Execute
> shiny::runApp()

Installation through Docker:

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