Welcome to the LENS documentation!

LENS (Landscape of Effective Neoantigen Software) is a tumor antigen discovery workflow capable of identifying potential therapeutic cancer immunotherapy targets from seven antigen sources.

The LENS manuscript is available here. LENS can be cited as:

Vensko II SP, et al. LENS: Landscape of Effective Neoantigens Software. Bioinformatics. 2023;39(6):btad322. doi:10.1093/bioinformatics/btad322

Note

New to LENS? Work through the user guide in order: Installing RAFT → Quick start (run the demonstration) → Preparing your samples → Running LENS using RAFT → Accessing and reviewing outputs → Using the report viewer → Interpreting the LENS reports.

For setup questions, defaults, and failure diagnosis, see Frequently asked questions, Troubleshooting, and the Off-the-shelf defaults reference page.

Getting started

• Introduction
• Quick start

User guide

• Installing RAFT
• Choosing your environment
• Preparing your samples
• Running LENS using RAFT
• Accessing and reviewing outputs
• Using the report viewer
• Interpreting the LENS reports
• Maintaining LENS projects

Help

• Frequently asked questions
  • RAFT and LENS
  • Running LENS
  • Workflow tools
  • Antigen sources
  • Algorithms
  • Reports
• Troubleshooting
  • Installation and environment
  • Manifest and sample setup
  • References and configuration
  • Runtime and execution
  • Hybrid and cloud issues
  • Outputs and report review

Contact

The development team can be reached using:

• Slack: https://join.slack.com/t/pirl-raft/shared_invite/zt-1y6mngjxf-VYLGMNiCFlXt9FabKcxw

• E-mail: steven_vensko@med.unc.edu