Copyright © 2022-2023 Sophie Colette. All Rights Reserved.
Title: Machine learning for organism growth temperature prediction and application of resampling methods to improve imbalanced data
Promotor: prof. Vera van Noort
Supervisor: Jaldert François
Each folder contains the code for part of the workflow:
Mining
: Web mining and integration with existing OGT databasesDatabase QC
: Quality assessment of the databasesGenome retrieval
: Extracting genomes for the species with available growth temperatureGenome Annotation
: Proteome predictions with Prokka and AugustusStability
: Feature stability analyses for the AA descriptors on protein and proteome levelData Analysis
: PCA and correlation analysesEmbeddings
: Extraction of ProtTrans and UniProt embeddingsModelling
: linear regression models + XGBoost, SVR and RF both without (random split and phylogenetic split) and with resamplingAgreement statistics
: Comparison of the predicted proteomes with UniProt reference proteomes