GeoMx analysis pipeline

This Snakemake pipeline analyzes the GeoMx data from the EyeMT project.

Table of Contents

• GeoMx analysis pipeline
  • Table of Contents
  • General Information
  • Features
  • Setup
  • Usage
  • Project Status
  • Room for Improvement
  • Acknowledgements
  • Contact
  • License

General Information

This pipeline processes the GeoMx expression data into gene regulatory networks using LIONESS and then performs the downstream analysis.

The entire pipeline is implemented using Snakemake. It will utilise a GPU to compute networks when available, but can also use CPUs only.

Features

The features already available are:

• Cleanup of expression data and prior networks
• Generation of LIONESS networks
• Comparison of experimental groups
• GSEA calculation
• Volcano plots

Setup

The requirements are provided in a requirements.txt file.

Usage

Running a Snakemake pipeline is straightforward:

snakemake --cores=10 --resources gpus=1

It is assumed that all the input is present and that the settings in the config.yaml file are correct. Some of the relevant settings are:

• input_dir: the directory containing the input files
• expression_file: name of the gene expression file
• motif_file: name of the motif prior file
• ppi_file: name of the PPI prior file
• metadata_file: name of the metadata file
• gpu_id: the ID of GPU to use

Project Status

The project is: in progress.

Room for Improvement

Room for improvement:

• Fix issues with the volcano plot labels
• Specification of comparisons in the config file

To do:

• Paired analysis with limma
• Final report
• Container

Acknowledgements

Many thanks to the members of the Kuijjer group at NCMBM/UH for their feedback and support.

This README is based on a template made by @flynerdpl.

Contact

Created by Ladislav Hovan ([email protected]). Feel free to contact me!

License

This project is open source and available under the GNU General Public License v3.