IMPORTANT: MethylR web-server moved from methylr.research.liu.se to https://methylr.serve.scilifelab.se/

methylr: a single shiny solution from sequencer data to pathway analysis

• Description
• Diagram
• Quick start
  • test data
  • local run
    • requirements
    • run command
• Step-by-step guide
• Workflow summaries
  • User input data preparation
  • input dataset
  • component tools
• Additional notes
• HELP/FAQ/Troubleshooting
• License(s)
• Acknowledgement
• Citation
• Credits

Description

For non-commercial Academic and Research purpose only! \ Here we introduce methylR, a complete pipeline for the analysis of both 450K and EPIC Illumina arrays which not only offers data visualization and normalization but also provide additional features such as the annotation of the genomic features resulting from the analysis, pairwise comparisons of DMCs with different graphical representation plus functional and pathway enrichment as downstream analysis, all packed in a minimal, elegant and intuitive graphical user interface which brings the analysis of array DNA methylation data.

Diagram

Quick start

Test data

1. All required test data except DNA methylation raw files, can be found here \ i. testDataFile1 - differentially methylated data file, can be used for gene features, Volcano plot, chromosome map, gene ontology and pathway enrichment analysis modules. \ ii. testDataFile2 - normalized beta value data table, can be used for MDS, PCA plots. PCA plot requires additional group data information, 'groupData'. \ iii. heatmapMatrix - heatmap matrix test data file added in the testdata directory.

2. DNA methylation test data can be found here

Local use:

We provide Docker container for local use. Please note, the docker container was built on AMD64 OS architecture to get the full functional capabilities of Shiny/R.

Computational requirements/compatibility (AMD64 only)

• LinuxOS - (AMD64)
  • Ubuntu 20.04LTS
  • Docker (version 20.10.18)
  • web-browser: Firefox (version 105)
• MacOS - (Intel, AMD64 only)
  • Monterey (version 12.5.1)
  • Docker (version 20.10.17)
  • Docker Desktop (version 4.12.0)
  • web-browsers:
    • Google Chrome (version 106),
    • Firefox (version 106),
    • Apple Safari (version 15.6.1)
• WindowsOS - (AMD64)
  • Windows 10 (version 21H2)
  • Docker (version 20.10.20)
  • Docker Desktop (version 4.13.0)
  • WSL2 - (Ubuntu 20.04LTS)
  • web-browsers:
    • Firefox (version 106),
    • Google Chrome (version 107),
    • Microsoft Edge (version 106).

PLEASE NOTE: the ARM64 chipset architecture is actually not supported by methylR.

Run the app

Linux AMD64 OS architecture

Step:1 - from terminal

# with docker container
docker run --rm -p 3838:3838 jd21/methylr:latest

Step:2 - web-browser

Open the web-browser (check above for your OS), and type:

http://localhost:3838

For Singularity container Thanks to WiilieYu (https://github.com/JD2112/methylr/issues/3), we found a problem on running Singularity/Apptainer container on methylR and using a script from sigularity-shiny, we solved the issue. Please run the commands below for Singularity container (tested with Singularity v3.8.6) -

1. To run the Singularity or Apptainer, please use the following commandlines -

# Copy prepare_template.sh to <YOUR_LOCAL_PATH> and run
/bin/bash prepare_template.sh start

The above command run will generate an script on the terminal and command to run on the server,

$ /bin/bash prepare_template.sh start
Generating shiny configuration...
port: 15910 # PLEASE NOTE THIS WILL BE CHANGED IN YOUR COMPUTER
logs: /tmp/shiny-server.ie3djR
base: /srv/shiny-server
run_as: jyotirmoy #<YOUR_USER_NAME>
Server logging will be in /tmp/shiny-server.ie3djR

To run your server:

    singularity run --bind /tmp/shiny-server.ie3djR/logs:/var/log/shiny \
    --bind /tmp/shiny-server.ie3djR/lib:/var/lib/shiny-server \
    --bind shiny-server.conf:/etc/shiny-server/shiny-server.conf <CONTAINER>

    ---------------------------------------------------------------------------
    For custom applications, also add --bind /srv/shiny-server:/srv/shiny-server
    To see your applications, open your browser to http://127.0.0.1:15910 or
    open a ssh connection from your computer to your cluster.

2. Run the following command on your server

singularity run --bind /tmp/shiny-server.ie3djR/logs:/var/log/shiny \
    --bind /tmp/shiny-server.ie3djR/lib:/var/lib/shiny-server \
    --bind shiny-server.conf:/etc/shiny-server/shiny-server.conf docker://jd21/methylr:latest

3. The terminal will prompt likes

   INFO:    Using cached SIF image
   INFO:    Converting SIF file to temporary sandbox...
   [2023-07-31T06:44:52.258] [INFO] shiny-server - Shiny Server v1.5.18.979 (Node.js v12.22.6)
   [2023-07-31T06:44:52.259] [INFO] shiny-server - Using config file "/etc/shiny-server/shiny-server.conf"