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/.

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/