Explore projects

This is a mirror from https://github.com/BarlierC/RNetDys.

This repository contains the code for ML analyses performed in Chapter 4 of my PhD thesis "Interpretable Machine Learning on omics data for biomarker discovery in Parkinson's disease". The project consists on performing Parkinson's disease (PD) case-control classification from blood plasma metabolomics measurements at the baseline clinical visit from the LuxPARK cohort, and from whole blood transcriptomics data at baseline as well as dynamic features engineered from a short temporal series of 4 timepoints from the PPMI cohort. The study involves evaluation of different feature selection strategies, The goal was to build and test a collection of ML models and, most interestingly, identify molecular and higher-level functional representations associated with PD diagnosis.

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

Method testing and analyses of Oxford Nanopore Technology (ONT) sequencing runs Data obtained by sequencing "generous donor B" across several runs Original data prepared by Rashi (post-sequencing) Initial analyses performed by CCL

A project for interactions with PubChem

Integrated Network approach for Cellular Transitions through SIgnalling MOlecules

Gene regulation inference of COVID-19

All scripts used for AMR and MGE analysis of the LAO dataset

R code for an interface to MINERVA API and helper functions

Utilities that work with GNPS records.

Playground for experiments on the official http://bioconductor.org/packages/devel/bioc/html/RMassBank.html

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