semvec/pypi-packages huggingface dataset:
SNAF 0.7.0
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)
Requires Python: >=3.7

[![Documentation Status](https://readthedocs.org/projects/snaf/badge/?version=latest)](https://snaf.readthedocs.io/en/latest/?badge=latest)  [![Pypi](https://img.shields.io/pypi/v/snaf?logo=PyPI)](https://pypi.org/project/snaf/)  [![Downloads](https://pepy.tech/badge/snaf)](https://pypi.org/project/snaf/)  [![Stars](https://img.shields.io/github/stars/frankligy/SNAF)](https://github.com/frankligy/SNAF/stargazers)

# 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).

![workflow](./images/fig1.png)


# Tutorial and documentation

[Full Documentation](https://snaf.readthedocs.io)

# Interactive Viewers (below, take a few seconds to load)

<p float="left">
  <img src="images/T_viewer.gif" width="45%" />
  <img src="images/B_viewer.gif" width="45%" /> 
</p>

# 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.


# Citation

[Guangyuan Li, Nathan Salomonis. SNAF: Accurate and compatible computational framework for identifying splicing derived neoantigens [abstract]. Cancer Res 2022;82(12_Suppl)](https://aacrjournals.org/cancerres/article/82/12_Supplement/1898/701846/Abstract-1898-SNAF-Accurate-and-compatible)

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