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 Configuration file)
- 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 the 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.