Gonçalves lab @ TU Delft

All

7 repositories

XCRISP
Public
X-CRISP: Domain-Adaptable and Interpretable CRISPR Repair Outcome Prediction by Seale C and Gonçalves JP (bioRxiv 2025)
machine-learning crispr transfer-learning domain-adaptation dna-repair dna-repair-outcome-prediction
Jupyter Notebook
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Other
•0•1•0•0•Updated Feb 17, 2025Feb 17, 2025
SBSL
Public
SBSL: Selection Bias-resilient Synthetic Lethality prediction models by Seale CF, Tepeli YI, Gonçalves JP (Bioinformatics 2022)
machine-learning selection-bias synthetic-lethality
R
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GNU General Public License v3.0
•1•2•0•0•Updated Feb 17, 2025Feb 17, 2025
MUSICiAn
Public
MUSICiAn: Genome-wide Identification of Genes Involved in DNA Repair via Control-Free Mutational Spectra Analysis by Seale CF, Barazas M, van Schendel R, Tijsterman M, and Gonçalves JP (bioRxiv 2025)
outlier-detection crispr mutational-signatures dna-repair gene-perturbation mutational-patterns mutational-spectra
Jupyter Notebook
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GNU General Public License v3.0
•0•1•0•0•Updated Feb 13, 2025Feb 13, 2025
Metric-DST
Public
Metric-DST: Mitigating Selection Bias Through Diversity-Guided Semi-Supervised Metric Learning by Tepeli YI, de Wolf M, and Gonçalves JP (arXiv 2024)
diversity machine-learning semi-supervised-learning metric-learning domain-adaptation fairness-ml selection-bias
Python
•0•1•0•0•Updated Nov 29, 2024Nov 29, 2024
DCAST
Public
DCAST: Diverse Class-Aware Self-Training for Fairer Learning by Tepeli YI and Gonçalves JP (arXiv 2024)
diversity machine-learning semi-supervised-learning self-training domain-adaptation fairness-ai fairness-ml selection-bias
Python
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GNU General Public License v3.0
•0•1•0•0•Updated Jul 31, 2024Jul 31, 2024
ELISL
Public
ELISL: Early-Late Synthetic Lethality Prediction in Cancer by Tepeli YI, Seale C, Gonçalves JP (bioRxiv 2022, Bioinformatics 2023)
machine-learning cancer selection-bias sequence-embeddings synthetic-lethality patient-survival-analysis
Python
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GNU General Public License v3.0
•0•4•0•0•Updated Apr 22, 2024Apr 22, 2024
SNMF
Public
SNMF: Integrated Learning of Mutational Signatures and Prediction of DNA Repair Deficiencies by Goossens S, Tepeli YI, Seale C, and Gonçalves JP (bioRxiv 2024)
crispr nonnegative-matrix-factorization mutational-signatures dna-repair gene-perturbation supervised-nmf
Python
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BSD 2-Clause "Simplified" License
•0•2•0•0•Updated Feb 21, 2024Feb 21, 2024