An online application that is designed to facilitate the exploration and thorough analysis of candidate genomic regions under selection, generating useful summary reports of prioritized variants that are putatively causal of recent selective sweeps. It compiles and graphically represents selection statistics based on linkage disequilibrium, a comprehensive set of functional annotations, and recent genealogical estimations of variant age for SNVs of the 26 populations of the phase 3 of the 1000GP.
Table of Contents
PopHumanVar is an interactive online application that is designed to facilitate the exploration and thorough analysis of candidate genomic regions under selection, generating useful summary reports of prioritized variants that are putatively causal of recent selective sweeps.
Available at: https://pophumanvar.uab.cat/
PopHumanVar is based on the Shiny framework for development of web-based applications using the R programming environment. Interactive plots are implemented with plotly. Interactive tables are generated with DT, an R-based interface to the JavaScript DataTables library. The genome browser integrated into the Summary Report section is implemented using the JBrowseR package. User queries are processed by R and sent to a MariaDB database.
PopHumanVar is served with Apache on a CentOS 7.2 Linux x64 server with 16 Intel Xeon 2.4 GHz processors and 32 GB RAM. All data, tools and support resources provided by the PopHumanVar database are open and freely available at https://pophumanvar.uab.cat. PopHumanVar is accessible and legible on computer, phone and tablet screens.
The PopHumanVar interface is divided into four main sections: (i) Stats Visualization represents the main navigation interface and provides several interactive graphs to aid the exploration and prioritization of genomic variants in the region of interest (Figure 2); (ii) Download provides tools to customize batch downloads from the database; (iii) Upload Data allows uploading and analyzing a VCF file with custom data; and (iv) Tutorial describes the database and presents a step-by-step usage example.
Check the tutorial.
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- scripts: here you will find all scripts used to get the information displayed in PopHumanVar
- createDb.sh
- genome_wide_isafe.py
- gwas_catalog.py
- isafe_windows.sub
- isafe_windows_1.txt
- isafe_windows_2.txt
- nsl.R
- run_pvals.py
- slider_new.R
- slidingWindowsToCondor.py
- snpeff.sh
- upload_data: scripts used to process the users data. There is also and example of the result they get on the email.
- www: here are stored all the imatges used in PopHumanVar tutorial, as well as in the article
- Fig_NN.png (from the tutorial)
- PopHumanVar_NN.png (from the article)
- README.md this file (hi!)
- .gitignore
- aboutUs_text.html: html used in the About Us section from the app
- intro_text.html: html from the popup every time the app runs
- tutorial_text.html: html with the tutorial informaiton
- helpSteps.csv: steps that appear at the top right information dialogue in the app
- global.R: packages & functions, run once before your app starts, any objects here are available to ui.R and server.R files respectively
- ui.R: users interface
- server.R: internal funcitons
See the open issues for a full list of proposed features (and known issues).
Please cite this reference for results obtained with PopHumanVar:
Aina Colomer-Vilaplana, Jesús Murga-Moreno, Aleix Canalda-Baltrons, Clara Inserte, Daniel Soto, Marta Coronado-Zamora, Antonio Barbadilla, Sònia Casillas (2021) PopHumanVar: an interactive application for the functional characterization and prioritization of adaptive genomic variants in humans. Nucleic Acids Research, Advance access gkab925 (https://doi.org/10.1093/nar/gkab925)
PopHumanVar was created at the Genetics and Microbiology Department and Institute of Biotechnology and Biomedicine of Universitat Autònoma de Barcelona by Aina Colomer i Vilaplana and Jesús Murga Moreno, PhD Students.
- May be used for commercial purposes
- May be used for private purposes
- May be modified, although:
- Modifications must be released under the same license when distributing the package
- Changes made to the code must be documented
- May be distributed, although:
- Source code must be made available when the package is distributed
- A copy of the license and copyright notice must be included.
- Comes with a LIMITATION of liability
- Comes with NO warranty
The authors would like to thank the Port d’Informació Científica (PIC) of the UAB for providing the informatics infrastructure in which most of the population genomics statistics have been computed, and help on using it. We also thank Esteve Sanz for providing some data management utilities, Laia Carrillo for evaluating the PopHumanVar data on several case regions, and members of the Genomics, Bioinformatics and Evolutionary Biology group for testing the database implementation. Finally, we thank two anonymous referees for very helpful comments on the PopHumanVar implementation and manuscript.
- Aina Colomer i Vilaplana
- Email: aina.colomer@uab.cat
- Sònia Casillas
- Email: sonia.casillas@uab.cat · Tel: +34 93 581 2730 · Fax: +34 93 581 2011
- Bioinformatics for Genomics Diversity group
- Department of Genetics and Microbiology · Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona Spain
- Institut de Biotecnologia i de Biomedicina · Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona Spain
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