Git Product home page Git Product logo

pvactools's Introduction

pVACtools

pVACtools is a cancer immunotherapy suite consisting of the following tools:

pVACseq

A cancer immunotherapy pipeline for identifying and prioritizing neoantigens from a list of tumor mutations.

pVACfuse

A tool for detecting neoantigens resulting from gene fusions.

pVACvector

A tool designed to aid specifically in the construction of DNA vector-based cancer vaccines.

Coming Soon

pVACclient

A browser-based user interface that assists users in launching, managing, reviewing, and visualizing the results of pVACtools processes.

pVACapi

The pVACapi will provide a HTTP REST interface to the pVACtools suite.

Citation

Jasreet Hundal, Beatriz M. Carreno, Allegra A. Petti, Gerald P. Linette, Obi L. Griffith, Elaine R. Mardis, and Malachi Griffith. pVAC-Seq: A genome-guided in silico approach to identifying tumor neoantigens. Genome Medicine. 2016, 8:11, DOI: 10.1186/s13073-016-0264-5. PMID: 26825632.

License

This project is licensed under NPOSL-3.0.

Installation

pVACtools requires Python 3.5. Before running any installation steps check the Python version installed on your system:

python -V

If you don’t have Python 3.5 installed, we recommend using Conda to emulate a Python 3.5. environment. We’ve encountered problems with users that already have Python 2.x installed when they also try to install Python 3.5. The defaults will not be set correctly in that case. If you already have Python 2.x installed we strongly recommmend using Conda instead of installing Python 3.5 locally.

Once you have set up your Python 3.5 environment correctly you can use pip to install pVACtools. Make sure you have pip installed. pip is generally included in python distributions, but may need to be upgraded before use. See the instructions for installing or upgrading pip.

After you have pip installed/upgraded, type the following command on your Terminal:

pip install pvactools

You can check that pVACtools has been installed under the default environment by listing all installed packages:

pip list

You can also check the installed version:

pvactools -v

pip will fetch and install pVACtools and its dependencies for you. After installing, each tool of the pVACtools suite is available with its own command line tree directly from the Terminal.

If you have an old version of pVACtools installed you might want to consider upgrading to the latest version:

pip install pvactools --upgrade

Documentation

The pVACtools documentation can be found on ReadTheDocs.

Contact

Bug reports or feature requests can be submitted on the pVACtools Github page. You may also contact us by email at [email protected].

pvactools's People

Contributors

agraubert avatar amberzw avatar chrisamiller avatar jasonwalker80 avatar jhundal avatar jmcmichael avatar jneich avatar malachig avatar mrjosh-zz avatar obigriffith avatar ryanking avatar susannasiebert avatar tmooney avatar willmclaren avatar yang-yangfeng avatar

Watchers

 avatar

Recommend Projects

  • React photo React

    A declarative, efficient, and flexible JavaScript library for building user interfaces.

  • Vue.js photo Vue.js

    🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.

  • Typescript photo Typescript

    TypeScript is a superset of JavaScript that compiles to clean JavaScript output.

  • TensorFlow photo TensorFlow

    An Open Source Machine Learning Framework for Everyone

  • Django photo Django

    The Web framework for perfectionists with deadlines.

  • D3 photo D3

    Bring data to life with SVG, Canvas and HTML. 📊📈🎉

Recommend Topics

  • javascript

    JavaScript (JS) is a lightweight interpreted programming language with first-class functions.

  • web

    Some thing interesting about web. New door for the world.

  • server

    A server is a program made to process requests and deliver data to clients.

  • Machine learning

    Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.

  • Game

    Some thing interesting about game, make everyone happy.

Recommend Org

  • Facebook photo Facebook

    We are working to build community through open source technology. NB: members must have two-factor auth.

  • Microsoft photo Microsoft

    Open source projects and samples from Microsoft.

  • Google photo Google

    Google ❤️ Open Source for everyone.

  • D3 photo D3

    Data-Driven Documents codes.