ExpHunter Suite Examples

This repository includes code to generate synthtetic results published in paper "Analysing rare disease model datasets with the ExpHunter Suite".

Also, supplementary files for this paper are stored here.

Synthetic Experiments

In order to replicate these experiments you must:

1. Install and configure your R environment as is explained in https://github.com/seoanezonjic/ExpHunterSuite
2. Configure launch.sh to include your environment load and your experiments results folder
3. Execute launch.sh

Once execution has finished:

4. Configure get_results.sh to include your environment load and your experiments results folder.
5. Execute get_results.sh

A new HTML file with the results report must has been generated

Important: this scripts uses Autoflow, be sure to has it installed in your system (https://github.com/seoanezonjic/autoflow)

Lafora / PMM2

In order to replicate these experiment (Lafora or PMM2) you must:

1. Install and configure your R environment as is explained in https://github.com/seoanezonjic/ExpHunterSuite
2. Execute file launch_DEgenesHunter.sh stored in specific folder.

Spike-ins

In order to replicate these experiments you must:

1. Install and configure your R environment as is explained in https://github.com/seoanezonjic/ExpHunterSuite
2. Configure your download folder and your JSON credential in ncbi_sra_file_downloader.sh. If you don't habe a NCBI credential, check this link https://www.ncbi.nlm.nih.gov/home/develop/https-guidance/
3. Once files have been downloaded, execute conversion configuring variables in conversion_loop.sh and execute.
4. At this point, you must use a clean&map program to transform fastq files into count tables.
5. Use count tables obtained to execute DEgenes Hunter expression analysis as done in Lafora or PMM2 but changing input file.