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lsru_bionfo / pipeline_16s
MIT LicenseUpdated -
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LCSB-BioCore / publications / KratochvilWilken24 - COBREXA2.0
Apache License 2.0Updated -
Environmental Cheminformatics / ShinyTPs
Artistic License 2.0ShinyTPs: Curate transformation products from text mining results from HSDB & PubChem
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Laura Denies / PathoFact
GNU General Public License v3.0 or laterUpdated -
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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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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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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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.
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ESB / ONT_pilot_gitlab
GNU General Public License v3.0 or laterMethod 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 CCLUpdated -
Environmental Cheminformatics / PubChem Docs
Artistic License 2.0A home for documentation, scripts etc related to PubChem efforts
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An exploration on gene expression data was carried out on single-cell RNAseq analyses of bronchoalveolar lavages from nine COVID-19 patients, three moderate cases, severe case and critical cases, comparing with healthy subjects.
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DVB / Monzel_2020
Apache License 2.0Updated -
Marina Popleteeva / courses
Creative Commons Zero v1.0 UniversalRepository for all slides related to R3 courses.
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This GitLab folder provides the scripts that were used in my Master Thesis Project. For any types of questions, please feel free to contact me.
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TNG / papers / PD GBM Publication
Apache License 2.0Updated -
LCSB-BioCore / publications / Hemedan 2023-Boolean modelling of PD
Apache License 2.0Updated