EGG: Epitope Generation Gateway
A modular Snakemake pipeline for personalized neoantigen discovery and prioritization using patient-specific gene co-expression networks.
Overview
EGG is a comprehensive computational workflow for identifying and prioritizing tumor neoantigens from DNA and RNA sequencing data. Unlike traditional neoantigen prediction pipelines that focus solely on ...
Type: Snakemake
Creators: Luca Mannino, Michele Fratello, Jacopo Chiaro, Federica D'Alessio, Emanuele Di Lieto, Miina Niittykoski, Angela Serra, Seppo Ylä-Herttuala, Vincenzo Cerullo, Antonio Federico, Dario Greco
Submitter: Luca Mannino
Prediction of HLA binding for verified candidates
Associated Tutorial
This workflows is part of the tutorial Neoantigen 5a: Predicting HLA Binding, available in the GTN
Features
- Includes a Galaxy Workflow Report
Thanks to...
...
Merging Fusion and non-normal databases + Discovery peptidomics using FragPipe
Associated Tutorial
This workflows is part of the tutorial Neoantigen 2: Database merge and FragPipe discovery, available in the GTN
Features
- Includes a Galaxy Workflow Report ...
Create a protein Fusion database through the Arriba workflow
Associated Tutorial
This workflows is part of the tutorial Neoantigen 1a: Fusion-Database-Generation, available in the GTN
Features
- Includes a Galaxy Workflow Report ...
Validate the NeoAntigen Candidates from FragPipe discovery through the PepQuery Novel search
Associated Tutorial
This workflows is part of the tutorial Neoantigen 3: PepQuery2 Verification, available in the GTN
Features
- Includes a Galaxy Workflow Report ...
Annotating the novel peptides
Associated Tutorial
This workflows is part of the tutorial Neoantigen 4: Variant Annotation, available in the GTN
Features
- Includes a Galaxy Workflow Report
Thanks to...
Workflow Author(s): GalaxyP ...
Predict binding using IEDB and check novelty peptides with PepQuery
Associated Tutorial
This workflows is part of the tutorial Neoantigen 5b: IEDB binding PepQuery Validated Neopeptides, available in the GTN
Features
- Includes a Galaxy Workflow Report ...
Generating non-reference protein database for FragPipe discovery
Associated Tutorial
This workflows is part of the tutorial Neoantigen 1b: Non-Reference-Database-Generation, available in the GTN
Features
- Includes a Galaxy Workflow Report ...
Annotating the novel peptides
Associated Tutorial
This workflows is part of the tutorial Neoantigen 5: Variant Annotation, available in the GTN
Features
- Includes a Galaxy Workflow Report
Thanks to...
Workflow Author(s): ...
Create a protein Fusion database through the Arriba workflow
Associated Tutorial
This workflows is part of the tutorial Neoantigen 1: Fusion-Database-Generation, available in the GTN
Features
- Includes a Galaxy Workflow Report ...
Generating non-reference protein database for FragPipe discovery
Associated Tutorial
This workflows is part of the tutorial Neoantigen 2: Non-Reference-Database-Generation, available in the GTN
Features
- Includes a Galaxy Workflow Report ...
Prediction of HLA binding for verified candidates
Associated Tutorial
This workflows is part of the tutorial Neoantigen 6: Predicting HLA Binding, available in the GTN
Features
- Includes a Galaxy Workflow Report
Thanks to...
...
Validate the NeoAntigen Candidates from FragPipe discovery through the PepQuery Novel search
Associated Tutorial
This workflows is part of the tutorial Neoantigen 4: PepQuery2 Verification, available in the GTN
Features
- Includes a Galaxy Workflow Report ...
Merging Fusion and non-normal databases + Discovery peptidomics using FragPipe
Associated Tutorial
This workflows is part of the tutorial Neoantigen 3: Database merge and FragPipe discovery, available in the GTN
Features
- Includes a Galaxy Workflow Report ...
Predict binding using IEDB and check novelty peptides with PepQuery
Associated Tutorial
This workflows is part of the tutorial Neoantigen 7: IEDB binding PepQuery Validated Neopeptides, available in the GTN
Features
- Includes a Galaxy Workflow Report ...
