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UROPA/docs_rst/index.rst

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Welcome to the UROPA documentation!

https://img.shields.io/badge/Install%20with-conda-green.svg?style=plastic&logoWidth=40 https://badge.fury.io/py/uropa.png

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, besthits)
  • 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: Kondili M, Fust A, Preussner J, Kuenne C, Braun T, Looso M. UROPA: a tool for Universal RObust Peak Annotation. Scientific Reports. 2017;7:2593. doi:10.1038/s41598-017-02464-y.

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
   uropa-example
   custom
   license
   help