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MOD-Finder

MOD-Finder (Multi-Omics Data set Finder) is an easy-to-use R Shiny app to efficiently search for compound-related data sets on the transcriptomic, proteomic, and metabolomic layer.

The webapp is available at UFZ, but the code can be run as a local stand-alone application. To do so, just clone this repository and follow the instructions described under 'Prerequisites'.

Prerequisites

Before the application can be started locally, some requirements have to be met. First, MOD-Finder was developed in a specific conda environment to avoid changing R package to infer with the functionality and stability of MOD-Finder. Second, MOD-Finder relies on public online sources that are subject to changes once in a while. But since not all of these sources provide sufficient access via RESTful APIs for example, MOD-Finder needs several local database files that have to be generated in advance.

Conda environment

To ensure reproducibility and functionality of MOD-Finder, we encourage all users to run the app in the provided conda environment. The environment can be created and activate by

conda env create -f mod_finder_conda.yml
source activate mod_finder

Creating local database files

These database files are essential for MOD-Finder in order to function properly. Before the apps is started for the first time, three different database files have to be present:

  • comptox.RData
  • CTD_chemicals.RData
  • GEOmetadb.sqlite

The first file comptox.RData is essential for the digital identification of chemicals of interest and contains an ID mapping of more than ??? thousand chemicals, including for example Pubchem IDs, CAS RN, and Comptox IDs. CTD_chemicals is the preprocessed source for retrieving chemical-specific information about effects on gene expression, pathway perturbations, and associations to diseases. GEOmetadb.sqlite contains the current version of the NCBI Geo database in an SQL format.

To create these database files in advance type the following commands:

cd /path/to/app/
mkdir data/
bash scripts/create_local_databases.sh data/

How to Cite

When you find MOD-Finder useful, please make sure to cite us accordingly: still to come