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README.md

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-# UROPA_GUI
-The Rshiny UROPA GUI App 
+## 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]( https://uropa-manual.readthedocs.io/config.html)
+-	**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 http://loosolab.mpi-bn.mpg.de/apps/UROPA.
+
+The source code of the underlying UROPA command line application can be downloaded at https://github.molgen.mpg.de/loosolab/UROPA under the MIT license. 
+
+An exhaustive manual can be found at https://uropa-manual.readthedocs.io/.
+
+Please make sure to check our other projects at http://loosolab.mpi-bn.mpg.de/.
+
+### Try UROPA GUI
+The [web server](http://loosolab.mpi-bn.mpg.de/apps/UROPA) contains all necessary data to quickly sample the capabilities of UROPA GUI.
+-  **UROPA 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.