pVACtools ========= pVACtools is a cancer immunotherapy tools suite consisting of the following tools: **pVACseq** A cancer immunotherapy pipeline for identifying and prioritizing neoantigens from a VCF file. **pVACbind** A cancer immunotherapy pipeline for identifying and prioritizing neoantigens from a FASTA file. **pVACfuse** A tool for detecting neoantigens resulting from gene fusions. **pVACvector** A tool designed to aid specifically in the construction of DNA-based cancer vaccines. **pVACview** An application based on R Shiny that assists users in reviewing, exploring and prioritizing neoantigens from the results of pVACtools processes for personalized cancer vaccine design. .. image:: images/pVACtools_main-figure_v7.png :align: center :alt: pVACtools immunotherapy workflow Contents -------- .. toctree:: :maxdepth: 2 pvacseq pvacbind pvacfuse pvacvector pvacview .. toctree:: :maxdepth: 1 install tools frequently_asked_questions releases license citation contribute contact mailing_list New in Release |release| ------------------------ This is a minor feature release. It adds the following features: - This release adds support for two new prediction algorithms: BigMHC and DeepImmuno (`#1063 `_). BigMHC includes predictions for elution (BigMHC_EL) and immunogenicity (BigMHC_IM). DeepImmuno is a prediction algorithms for immunogenicty. - This release includes several updates to pVACview (`#1012 `_): - The tab containing the anchor heatmaps for each well-binding peptide of a variant has been moved to the "Transcript and Peptide Set Data" panel. - The anchor heatmap tab now also contains a table of all the per-length and per-allele anchor weights for each position in a peptide. - The pVACtools version is now displayed at the bottom of the sidebar. - A new panel has been added to show the tiering parameters currently applied. - Where there are multiple transcript sets for a variant, the one containing the best peptide is now selected by default. - This release adds a new command ``pvactools download_wdls`` (`#1055 `_). This command can be used to download WDL workflow files for pVACseq and pVACfuse. Past release notes can be found on our :ref:`releases` page. To stay up-to-date on the latest pVACtools releases please join our :ref:`mailing_list`. Citations --------- Jasreet Hundal , Susanna Kiwala , Joshua McMichael, Chris Miller, Huiming Xia, Alex Wollam, Conner Liu, Sidi Zhao, Yang-Yang Feng, Aaron Graubert, Amber Wollam, Jonas Neichin, Megan Neveau, Jason Walker, William Gillanders, Elaine Mardis, Obi Griffith, Malachi Griffith. pVACtools: A Computational Toolkit to Identify and Visualize Cancer Neoantigens. Cancer Immunology Research. 2020 Mar;8(3):409-420. doi: 10.1158/2326-6066.CIR-19-0401. PMID: `31907209 `_. Jasreet Hundal, Susanna Kiwala, Yang-Yang Feng, Connor J. Liu, Ramaswamy Govindan, William C. Chapman, Ravindra Uppaluri, S. Joshua Swamidass, Obi L. Griffith, Elaine R. Mardis, and Malachi Griffith. `Accounting for proximal variants improves neoantigen prediction `_. Nature Genetics. 2018, DOI: 10.1038/s41588-018-0283-9. PMID: `30510237 `_. Jasreet Hundal, Beatriz M. Carreno, Allegra A. Petti, Gerald P. Linette, Obi L. Griffith, Elaine R. Mardis, and Malachi Griffith. `pVACseq: A genome-guided in silico approach to identifying tumor neoantigens `_. Genome Medicine. 2016, 8:11, DOI: 10.1186/s13073-016-0264-5. PMID: `26825632 `_. Source code ----------- The pVACtools source code is available in `GitHub `_. License ------- This project is licensed under `BSD 3-Clause Clear License `_.