NTA for woman nurse and firefighters

The goal of this project is to realize Non targeted analysis for nurse
The pipeline is divided in 5 steps:

• Step 1: Women Worker Biomonitoring Chemical Database Development (v.2)
• Step 2: Non-targeted LC-QTOF/MSfull scan analysis procedure (and developing the features list)
• Step 3: Review of features and criteria to select features for fragmentation
• Step 4: Fragmentation and annotation
• Step 5: Chemical selection criteria for targeted confirmation and quantification

Please see the full pipeline in the py note book: xxxx

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Installation

Develop on Ubuntu-wsl on Windows 10 (wsl2 - ubuntu 20.4)

Dependencies

• python (3.9)
• biotransformer (http://biotransformer.ca/) => request java install
• request database.init for DTXSID search
• R (4.1.0)

Python libraries

• RDKit (> 3.1): http://rdkit.org/docs/index.html
• molVS (> 1): https://molvs.readthedocs.io/en/latest/index.html
• CompDesc ($pip install -i https://test.pypi.org/simple/ CompDesc)

R libraries + dependencies

• ncdf4 ($sudo apt-get install r-cran-ncdf4)
• libmagick ($sudo apt install libmagick++-dev)
• libxml2-dev ($sudo apt-get install libxml2-dev)
• libcurl4-openssl-dev ($sudo apt -y install libcurl4-openssl-dev)
• gsl ($sudo apt install r-cran-gsl)
• all of the libraries can be installed using the script: ./R/requirements.R