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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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Environmental Cheminformatics / PubChem Docs
Artistic License 2.0A home for documentation, scripts etc related to PubChem efforts
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Miroslav Kratochvil / minervaR
GNU General Public License v3.0 onlyR code for an interface to MINERVA API and helper functions
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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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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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Environmental Cheminformatics / PD cheminformatics pipeline
Artistic License 2.0Updated -
Computational modelling and simulation / GeneRegulationAnalysis
GNU Affero General Public License v3.0Gene regulation inference of COVID-19
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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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LCSB-BioCore / publications / Hemedan 2023-Boolean modelling of PD
Apache License 2.0Updated -
BDS / Ml Dyskinesia
MIT LicenseUpdated -
Menglin Zheng / SiPer
GNU Affero General Public License v3.0A computational method to identify signalling perturbations targeting specific sets of transcription factors for cellular conversion
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Jacek Lebioda / ChemPert
GNU Affero General Public License v3.0Updated -
Aurélien Ginolhac / drake-gitlab-docker
MIT LicenseUpdated -
ESB / ensemble_spieceasi
GNU General Public License v3.0 onlyNetwork Analyses - SpiecEasi The Rscripts and Snakefile herein can be used to run SpiecEasi for generating networks from taxonomic counts Dependencies snakemake >= 5.3.0 References (SpiecEasi)[https://github.com/zdk123/SpiecEasi]Updated