.. image:: images/pVACseq_logo_trans-bg_sm_v4b.png
    :align: right
    :alt: pVACseq logo

.. _pvacseq:

pVACseq
=======

pVACseq is a cancer immunotherapy pipeline for the identification of **p**\ ersonalized **V**\ ariant **A**\ ntigens by **C**\ ancer **Seq**\ uencing (pVACseq) that integrates tumor mutation and expression data (DNA- and RNA-Seq). It enables cancer immunotherapy research by using massively parallel sequence data to predicting tumor-specific mutant peptides (neoantigens) that can elicit anti-tumor T cell immunity. It is being used in studies of checkpoint therapy response and to identify targets for personalized cancer vaccines and adoptive T cell therapies. For more general information, see the `manuscript published in Genome Medicine <http://www.genomemedicine.com/content/8/1/11>`_.

.. toctree::
   :maxdepth: 2
   :glob:

   pvacseq/features
   pvacseq/input_file_prep
   pvacseq/getting_started
   pvacseq/run
   pvacseq/output_files
   pvacseq/filter_commands
   pvacseq/additional_commands
   pvacseq/optional_downstream_analysis_tools
   pvacseq/errors
   pvacseq/frequently_asked_questions