A Python package to predict, prioritize and visualize splicing derived neoantigens, including MHC-bound peptides (T cell antigen) and altered surface protein (B cell antigen)
Project description
SNAF
Splicing Neo Antigen Finder (SNAF) is an easy-to-use Python package to identify splicing-derived tumor neoantigens from RNA sequencing data, it can predict, prioritize and visualize MHC-bound neoantigen for T cell (T antigen) and altered surface protein for B cell (B antigen).
Tutorial and documentation
Input and Output
Simply put, user needs to supply a folder with bam files
, and the HLA type
assciated with each patient (using your favorite HLA typing tool). And it will generate predicted immunogenic MHC-bound peptides and altered surface protein. Moreover, there's a myriad of convenient function that enables users to conduct survival analysis, association analysis and publication-quality visualiztion. Check our tutorials for more detail.
Interactive Viewers
Citation
A preprint will be released soon.
Contact
Guangyuan(Frank) Li
Email: li2g2@mail.uc.edu
PhD student, Biomedical Informatics
Cincinnati Children’s Hospital Medical Center(CCHMC)
University of Cincinnati, College of Medicine
Project details
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