Shiny DNAmBenchmarking

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:

• Open an issue
• Or contact the maintainer directly