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 prerequisites are installed, follow steps below to build and 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
> install.packages("renv")
> renv::install("shiny")
> renv::install("bioc::SummarizedExperiment")
> renv::install("bioc::ComplexHeatmap")
> renv::install("tidyverse")
> renv::install("testthat")
> renv::install("shinyjs")
> renv::install("shinyalert")
> renv::install("svglite")
> renv::install("bioc::ensembldb")
> renv::install("bioc::EnsDb.Hsapiens.v86")
> renv::install("plotly")
> renv::install("shinyWidgets")
> renv::install("ggVennDiagram")
> renv::install("rhandsontable")
> renv::install("shinyBS")
> renv::install("shinycssloaders")
> renv::install("shiny.info")
> renv::install("fastcluster")
> renv::install("factoextra")
> renv::install("UpSetR")
> renv::install("vegan")
> renv::install("assertthat")

# Execute
> 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/