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samavinasir / proteoannot

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Standalone Python package for annotating protein sequences with biological and physicochemical properties (iFeature, IEDB, SignalP) for reverse vaccinology. Extracted from VacSol-ML(ESKAPE); supports multi-allele MHC-I/II epitope prediction. Provides both a Python API and a CLI

machine-learning bioinformatics machine-learning-algorithms proteomics signal-peptides bioinformatics-analysis python-package epitope-prediction-methods protein-annotation bioinformatics-tool epitope-prediction vaccine-design reverse-vaccinology mhc-binding-prediction protein-annotations proteomics-data-analysis signal-peptide iedb ifeature signal-peptide-detection
  • Updated Jul 30, 2026
  • Python

Qasim-Hussain-Code / peptide_mhc_binding_prediction

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HLA-A*02:01 nine-mer peptide binding prediction from sequence, with grouped validation and fully traceable metrics.

python machine-learning bioinformatics reproducible-research scikit-learn decision-trees hla data-quality immunoinformatics computational-immunology epitope-prediction interpretable-machine-learning vaccine-design neoantigen binding-affinity iedb peptide-mhc mhc-class-i
  • Updated Aug 16, 2026
  • Python

PundarikakshNTripathi / bias-controlled-neoantigen-immunogenicity-pipeline

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Bias-controlled evaluation protocol and pipeline for neoantigen immunogenicity prediction: matched HLA-only and peptide-only null controls, shortcut-dependence diagnostics, and a no-override acceptance gate.

python benchmark bioinformatics pytorch mhc reproducibility hla mutual-information computational-immunology neoantigen shortcut-learning evaluation-protocol immunogenicity-prediction iedb t-cell-epitope
  • Updated Oct 11, 2026
  • Python

Qasim-Hussain-Code / neoantigen_immunogenicity_prediction

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Chapter 6 of Machine Learning for Biology. Sequence-only immunogenicity prediction on 1,200 HLA-A*02:01 IEDB binders, cluster-split and pre-registered. Network 0.610 AUPRC, binding-only baseline 0.591, chance 0.485.

machine-learning bioinformatics tesla immunoinformatics computational-immunology neoantigen cancer-immunotherapy immunogenicity iedb t-cell-epitope peptide-mhc mhc-class-i hla-a0201
  • Updated Sep 20, 2026
  • Python

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