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This repository contains the code for ML analyses performed in Chapter 5 of my PhD thesis "Interpretable machine learning on omics data for the study of UPDRS III prognosis". The project consists on predicting the Unified Parkinson’s Disease Rating Scale Part III (UPDRS III) motor scores (mild/severe when classification) from whole blood transcriptomics and blood plasma metabolomics using measurements from the baseline clinical visit, and temporal or dynamic features engineered from a short temporal series of 4 and 3 timepoints, respectively, from the PPMI cohort and the LuxPARK cohort, aiming at identifying molecular and higher-level functional fingerprints linked specifically to the motor symptoms in PD.

Basic practice repository for git trainings

Pre-screening mass spectrometry data.

This repository contains the scripts that have been developed in the course of the GeneDER project (Biomedical Data Science group - Enrico Glaab Lab).

Benchmark scripts related to the COBREXA.jl publication

A project for interactions with PubChem

Integrated Network approach for Cellular Transitions through SIgnalling MOlecules

A new shiny interface to generate transformation products (TPs) from parent compounds (pesticides, pharmaceuticals, etc.).

This project hosts the JSON schemas used for representing the metadata of submissions to the ELIXIR translational data repository. It also provides validation utility methods.

The COVIDminer text mining project (https://rupertoverall.net/covidminer/) reads the published literature concerning SARS-CoV-2 and COVID-19 to extract statements about (primarily molecular) interactions. Using the API associated with this project, p

Basic practice repository for git trainings

A docker image with pre-installed requirements for running Jekyll, created in order to minimize the build time