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Elisa Gomezdelope / ML_PD_metab_transc
MIT LicenseThis 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.
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R3 / apps / generator
Apache License 2.0This project includes the generator scripts for generating the index files of the howto-cards and modules (handbook, qms, ...)
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Elisa Gomezdelope / ML_UPDRSIII_metab_transc
MIT LicenseThis 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.
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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.
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Jenny Thuy Dung Tran / basic-practice-pages
MIT LicenseBasic practice repository for git trainings
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Janine Schulz / basic-practice-pages
MIT LicenseBasic practice repository for git trainings
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Computational modelling and simulation / GeneRegulationAnalysis
GNU Affero General Public License v3.0Gene regulation inference of COVID-19
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R3 / apps / tailorbird / linkchecker
Apache License 2.0Updated -
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Carmen Lahr / basic-practice-pages
MIT LicenseBasic practice repository for git trainings. Carmen's fork.
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Jil Fischbach / basic-practice-pages
MIT LicenseBasic practice repository for git trainings
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IDERHA / DRS-cli
Apache License 2.0Client for GA4GH Data Repository Service (DRS) API service
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Marina Popleteeva / courses
Creative Commons Zero v1.0 UniversalRepository for all slides related to R3 courses.
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Graph representation learning modelling pipeline exploiting molecular interaction networks of transcriptomics (protein-protein interactions) and metabolomics (metabolite-metabolite interactions) to learn PD-specific fingerprints from the spatial distribution of molecular relationships in an end-to-end fashion. The scripts apply the graph representation learning modelling pipeline on networks of molecular interactions, where transcriptomics and metabolomics data from the PPMI and the LuxPARK cohort, respectively, are projected.
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LCSB-BioCore / publications / Hemedan 2023-Boolean modelling of PD
Apache License 2.0Updated -
Elisa Gomezdelope / GRL_sample_similarity_PD
MIT LicenseGraph 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.
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