From ff970638e970680a8df72670e3e745add73d5e02 Mon Sep 17 00:00:00 2001 From: mlooso Date: Thu, 25 Jan 2018 15:53:23 +0100 Subject: [PATCH] Update README.md --- README.md | 39 +++++++++++++++++++++++++++++++++++++-- 1 file changed, 37 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index e801540..e38ee26 100644 --- a/README.md +++ b/README.md @@ -1,2 +1,37 @@ -# 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.