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frankligy / SNAF

Splicing Neo Antigen Finder (SNAF) is an easy-to-use Python package to identify splicing-derived tumor neoantigens from RNA sequencing data, it further leverages both deep learning and hierarchical Bayesian models to prioritize certain candidates for experimental validation
MIT License
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filtering out B antigen candidates where predicted peptides fully contained in reference #11

Closed frankligy closed 2 years ago

frankligy commented 2 years ago
  1. make sure to label whether it is insertion or deletion, by comparing the length of peptide, just need to use canonical isoform reference
  2. whether the junction is on extracellular domain, use a look up table of extracelluar topological annotation
frankligy commented 2 years ago 
df = pd.read_csv('/Users/ligk2e/Downloads/Hs_FeatureCoordinate.txt',sep='\t',index_col=0)
df = df.loc[df['description']=='TOPO_DOM-Extracellula',:]
df.to_csv('/Users/ligk2e/Desktop/df_topology.txt',sep='\t')