JBR Genome Browser

Status: Active

JBR Genome Browser is a fast and scalable general purpose genome browsers with support of a novel semi-supervised approach to peak calling.

One of the major challenges of the semi-supervised learning is the procedural complexity of the manual annotation of the data, which often leads to the inaccuracies and mix-ups. We created a brand new visualization tool that would support classical genome browser capabilities and provide readily accessible integrated peak annotation and peak calling capabilities. JBR Genome Browser allows researchers to upload tracks of the Chip-seq data and perform on-the-fly annotation and peak calling for a given annotation, where results of the peak calling are immediately visualized as BED files in the same session. It can serve not only as an efficient semi-supervised peak calling engine but also as a next-generation genome browser. It provides enhanced capabilities for viewing large files, observing multiple locations simultaneously, and gathering track statistics.

Main features:

  • Supports semi-supervised peak calling with SPAN Peak Analyzer
  • Support for common track formats, e.g. WIG, BED, etc.
  • Capable to open saved IGV sessions
  • Support for combining tracks, i.e. arithmetic operations
  • Easy visualization of multiple genomic regions
  • Custom statistics tracks for multiple regions
  • Frontend-agnostic, can be used as a desktop application and web-service

Download here.

Participants

Publications

  • Irina Shchukina, Juhi Bagaitkar, Oleg Shpynov, Ekaterina Loginicheva, Sofia Porter, Denis A. Mogilenko, Erica Wolin, Patrick Collins, German Demidov, Mykyta Artomov, Konstantin Zaitsev, Sviatoslav Sidorov, Christina Camell, Monika Bambouskova, Laura Arthur, Amanda Swain, Alexandra Panteleeva, Aleksei Dievskii, Evgeny Kurbatsky, Petr Tsurinov, Roman Chernyatchik, Vishwa Deep Dixit, Marko Jovanovic, Sheila A. Stewart, Mark J. Daly, Sergey Dmitriev, Eugene M. Oltz & Maxim N. Artyomov
    Nature Aging,
  • Irina Shchukina, Juhi Bagaitkar, Oleg Shpynov, Ekaterina Loginicheva, Sofia Porter, Denis A. Mogilenko, Erica Wolin, Patrick Collins, German Demidov, Mykyta Artomov, Konstantin Zaitsev, Sviatoslav Sidorov, Christina Camell, Monika Bambouskova, Laura Arthur, Amanda Swain, Alexandra Panteleeva, Aleksei Dievskii, Evgeny Kurbatsky, Petr Tsurinov, Roman Chernyatchik, Vishwa Deep Dixit, Marko Jovanovic, Sheila A. Stewart, Mark J. Daly, Sergey Dmitriev, Eugene M. Oltz, Maxim N. Artyomov
    bioRxiv preprint,
  • Oleg Shpynov, Aleksei Dievskii, Roman Chernyatchik, Evgeny Kurbatsky, Petr Tsurinov and Maxim Artyomov
    Proceedings of the 17th European conference on computational biology,
  • Oleg Shpynov, Aleksei Dievskii, Roman Chernyatchik, Evgeny Kurbatsky, Petr Tsurinov, Maxim N. Artyomov
    Proceedings of Biata2018 Bioinformatics: from algorithms to applications,