Explore projects

Computational models of different aspects of COVID-19

ELIXIR Luxembourg's GA4GH Beacon API implementation in Python

The back-end component of Fractalis.

STAR and DESeq2

Integrated meta-omics pipeline

Scheduling assignments for Parkinson Research Clinic

A project for interactions with PubChem

Additional analyses for IMP manuscript

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

Code used for the analysis of the RNA-seq, ATAC-seq and ChIP-seq datasets produced in this study. Original fastq files deposited in https://ega-archive.org/, under the accession number EGAD00001009288.

LAO time series analyses

Basic practice repository for git trainings

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.

Benchmark scripts related to the COBREXA.jl publication

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 project includes the generator scripts for generating the index files of the howto-cards and modules (handbook, qms, ...)