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Shiny DNAmBenchmarking

run with docker run with Singularity

Overview

This Shiny application allows users to visualize and analyze the results of the benchmarking study, providing an intuitive interface for exploring the data.

Background

DecoNFlow is a bioinformatics pipeline for computational deconvolution of DNA methylation data, supporting both reference-based and reference-free tools. Learn more: VIBTOBIlab/DecoNFlow.

Quick Start

1. Clone

git clone git@github.com:VIBTOBIlab/Shiny-DNAmBenchmarking.git
cd Shiny-DNAmBenchmarking/

2. Input format

By default het app loads results/benchmarking_dataset.csv. If you provide your own CSV, include these columns:

Column Name Description
sample Sample identifier
predicted_tf Predicted tumoral factor (TF) for the sample
deconv_tool Deconvolution tool used
tumor_type Tumor type
dmr_tool DMR method used
seq_depth Sequencing depth
mixture_type Type of mixture
seq_method Sequencing method
expected_tf Expected tumoral factor (TF) for the sample

Example (first rows):

sample,predicted_tf,deconv_tool,tumor_type,dmr_tool,seq_depth,seq_method,mixture_type,expected_tf
healthy_merged_BRCA_0.0001_310000000_rep1,0.025818,UXM,BRCA,wgbstools,310M,wgbs,in_silico,1.00E-04
healthy_merged_BRCA_0.0001_310000000_rep10,0.0057756,UXM,BRCA,wgbstools,310M,wgbs,in_silico,1.00E-04
healthy_merged_BRCA_0.0001_310000000_rep2,0.0138815,UXM,BRCA,wgbstools,310M,wgbs,in_silico,1.00E-04

Place your file at results/benchmarking_dataset.csv or bind-mount it as shown below.

3. Run the app

For more information, please refer to the docs/.

▶️ Docker

docker run -p 3838:3838 \
  -v "$(pwd)/results/benchmarking_dataset.csv":/home/app/results/benchmarking_dataset.csv \
  sofvdvel/rshiny-dnambenchmarking:v1

▶️ Singularity

singularity pull docker://sofvdvel/rshiny-dnambenchmarking:v1
singularity run \
  --bind "$(pwd)/results/benchmarking_dataset.csv":/home/app/results/benchmarking_dataset.csv \
  rshiny-dnambenchmarking_v1.sif

4. Open the app

After the container starts, open: http://localhost:3838.

Credits

The scripts and containers have been written and built by Sofie Van de Velde, who is also the maintainer.

Support

If you encounter any issues or have questions, please: