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    output
    uropa-example
    custom
+   uropa_gui
    license
    help
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+UROPA GUI
+==========
+
+**A Web Platform for genomic region annotation**
+ 
+The annotation of genomic ranges such as peaks resulting from ChIP-seq/ATAC-seq or other techniques represents a fundamental task of bioinformatics analysis with crucial impact on many downstream analyses. In our previous work, we introduced the Universal Robust Peak Annotator (UROPA), a flexible command line based tool which considerably extends the functionality of existing annotation software. In order to reduce the complexity for biologists and clinicians, we have implemented an intuitive web-based graphical user interface (GUI) and fully functional service platform for UROPA. This extension will empower all users to generate annotations for regions of interest interactively.
+
+Features
+---------
+
+* **Input**: BED file of peaks or other genomic regions
+* **Reference**: GTF file of desired target features (e.g. genes, transcripts, probes, repeats, ...); source = Gencode/Ensembl (102 organisms included) or custom upload
+* **Association rules**: VERY diverse and easily combinable to a complex ruleset (see :doc:`/config`)
+* **Persistence**: Unique identifier is created on the server and results will remain available temporarily using the respective link
+* **Hosted**: Either online on our web server or as a local R Shiny installation
+
+Availability and Implementation
+-------------------------------
+
+The open source UROPA GUI server was implemented in R Shiny and Python and is available from `UROPA_GUI`_ .
+Please make sure to check `loosolab`_ for a comprehensive overview of all our projects and implemented tools.
+
+Try UROPA GUI
+--------------
+
+The `UROPA_GUI`_ contains all necessary data to quickly sample the capabilities of UROPA GUI.
+*  **UROPA GUI user guide**: Stepwise tutorial.
+* **Example data**: The following demo GTF and BED files are available on the server. 
+      
+      Homo_sapiens.hg19.GRCh37.75_genes_v2.gft -> `Human GTF` file with reference genes
+      
+      ENCFF001VFA.pol2.sub.bed -> `POLR2A`_ ChIP-seq experiment (14989 peaks)
+
+..note::  It is mandatory to select filter.attribute before attribute.value. Depending on the GTF file, it might take some time for attribute.value to be loaded. Please be patient!
+
+How to cite
+------------
+
+* Kondili M, Fust A, Preussner J, Kuenne C, Braun T, and Looso M. UROPA: a tool for Universal RObust Peak Annotation. Scientific Reports 7 (2017), doi: https://www.nature.com/articles/s41598-017-02464-y
+* Hendrik Schultheis, Jens Preussner, Annika Fust, Mette Bentsen, Carsten Kuenne, Mario Looso: UROPA: A Web Platform for genomic region annotation
+
+License
+-------
+
+This project is licensed under the MIT license.
+
+.. _UROPA_GUI: http://loosolab.mpi-bn.mpg.de/apps/UROPA
+.. _loosolab: http://loosolab.mpi-bn.mpg.de/
+.. _POLR2A: https://www.encodeproject.org/experiments/ENCSR000EAD/
+.. _Human GTF: ftp://ftp.ensembl.org/pub/release-75/gtf/homo_sapiens/ 
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