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ShinyTPs: Curate transformation products from text mining results from HSDB & PubChem

CO-INFECTOMICS - identification of co-infections and other factors associated with COVID-19 severity in the gut microbiome

This repository contains the code for statistical analyses performed in Chapter 3 of my thesis "Cross-sectional and longitudinal profiling of PD transcriptomics and metabolomics". The project consists on whole blood transcriptomics and blood plasma metabolomics cross-sectional and longitudinal profiling of Parkinson's disease patients and controls from the PPMI cohort and the LuxPARK cohort respectively, to identify differential molecular and higher-level functional features in PD.

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

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.

A project for interactions with PubChem

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

Graph representation learning modelling pipeline exploiting sample-similarity networks derived from high-throughput omics profiles to learn PD-specific fingerprints from the spatial distribution of molecular abundance similarities in an end-to-end fashion. The scripts apply the graph representation learning modelling pipeline on sample-similarity networks of transcriptomics and metabolomics data from the PPMI and the LuxPARK cohort, respectively.

A home for documentation, scripts etc related to PubChem efforts

Repository for all slides related to R3 courses.