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UROPA/docs_rst/index.rst

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Welcome to the UROPA documentation!

UROPA is a command line based tool intended for genomic region annotation.

Advantages of UROPA

  • Detect the most appropriate annotation of peaks, utilizing parameters such as
    • feature type
    • feature anchor
    • feature direction relative to peak location
    • filtering for attribute values, e.g. “protein_coding”
    • strand specificity
  • Utilization of any available GTF files as annotation reference
  • Multiple queries can be processed in a single run
  • Graduated annotation due to prioritization
  • Multiple output tables (AllHits, FinalHits, BestperQuery_Hits)
  • Visual summary for annotation evaluation
  • Preparation of custom annotation files with the UROPA to GTF utility

How to cite

Please cite the paper describing UROPA when using it in your research: tba

PDF version

Choose master version for better pdf layout.

Hint

  • On the bottom right there is a drop down menu
  • click latest
  • click PDF

Contribute

Support

If you have any issue feel free to send an email to Mario Looso

Licence

The project is licensed under the MIT license (see :doc:`/license`)

.. toctree::
   :maxdepth: 3
   :caption: Content of this manual

   introduction
   install
   parameter
   config
   output-pdf
   uropa-example-pdf
   custom-pdf
   license
   help