1. Home
  2. Workflows
  3. HLA ligandomics workflow using OpenMS and ImmunoNodes

HLA ligandomics workflow using OpenMS and ImmunoNodes

Created: 2016-11-30 15:23:38      Last updated: 2017-04-11 18:51:47

HLA ligandomics workflow combining native KNIME, OpenMS, and ImmunoNodes nodes. The workflow extracts MS data from PRIDE and performs mass spectra identification with X!Tandem, annotates the results with details of the given target/decoy database, calculates false discovery rates and filters for 5% FDR using OpenMS’ nodes. The identified peptides are annotated with their respective binding affinity predicted by NetMHC using the EpitopePrediction node. Finally, simple summary statistics and visualizations are generated with the use of native KNIME nodes
<!--EndFragment-->

Information Preview

Medium

Information Run

Not available


Information Workflow Components

Not available

Information Workflow Type

KNIME

Information Uploader

Avatar Benjamin Schubert

Information License

All versions of this Workflow are licensed under:

BSD License

Information Version 1 (earliest) (of 2)

View version:

Information Credits (1)

(People/Groups)

Information Attributions (0)

(Workflows/Files)

None

Information Tags (0)

None

Log in to add Tags

Information Shared with Groups (0)

None

Information Featured In Packs (0)

None

Log in to add to one of your Packs

Information Attributed By (0)

(Workflows/Files)

None

Information Favourited By (0)

No one

Information Statistics

1887 viewings

647 downloads

[ see breakdown ]

More
 

Citations (0)

None


Version History

In chronological order:

  1. HLA ligandomics workflow using OpenMS and ImmunoNodes

    Created by Benjamin Schubert on Wednesday 30 November 2016 15:23:38 (UTC)

    Last edited by Benjamin Schubert on Thursday 30 March 2017 14:40:03 (UTC)

  2. HLA ligandomics workflow using OpenMS and ImmunoNodes

    Created by Benjamin Schubert on Tuesday 11 April 2017 18:51:27 (UTC)

    Last edited by Benjamin Schubert on Tuesday 11 April 2017 18:51:47 (UTC)



Reviews Reviews (0)

No reviews yet

Be the first to review!



Comments Comments (0)

No comments yet

Log in to make a comment




Workflow Other workflows that use similar services (0)

There are no workflows in myExperiment that use similar services to this Workflow.

Funded by: BioVeL, EPSRC, JISC, Microsoft

Affiliates: myGrid, Taverna, BioCatalogue
About | Privacy | Publications | Contact / Feedback | Mailing List
Icons: Silk icon set 1.3

Copyright © 2007 – 2018 The University of Manchester and University of Southampton