JBR Genome Browser is a fast and scalable general purpose genome browser with support of a novel semi-supervised approach to peak calling.
It supports classic genome browser functionality and provide readily accessible integrated peak annotation and peak calling capabilities. JBR Genome Browser allows researchers to upload tracks of Chip-seq data and perform on-the-fly annotation and peak calling with SPAN algorithm for a given annotation, with the results of peak calling 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 with enhanced functionality for viewing large files, viewing multiple locations simultaneously, and gathering track statistics.
Open Access Paper: https://doi.org/10.1093/bioinformatics/btab376
Citation: Shpynov O, Dievskii A, Chernyatchik R, Tsurinov P, Artyomov MN. Semi-supervised peak calling with SPAN and JBR Genome Browser. Bioinformatics. 2021 May 21.
Note: JBR Genome Browser supports models produced by the SPAN version 1.0+.
See releases section for actual information.
See changelog for the latest version here.
Download a suitable build for your OS from the Downloads section.
Windows
Unpack the browser jbr-XXX.zip
file.
Launch jbr.exe
.
MacOS
Download the jbr-XXX.dmg
macOS Disk Image file
Mount it as another disk in your system
Copy JBR Genome Browser to your Applications folder
If you want to open multiple JBR instances, launch instance with the command:
open -n "/Applications/JBR XXX.app"
Linux:
Unpack the browser jbr-XXX.tar.gz
file using the following command:
tar -xzf jbr-XXX.tar.gz
Launch jbr.sh
from the bin
subfolder.
JBR Genome Browser can be set up as a local web server which allows for an accessible way to share the results. This can
be particularly useful when working with private datasets, which cannot be exported to public UCSC browser session, and
should be accessible only within local network.
Example of web server mode can be seen at: https://artyomovlab.wustl.edu/jbr/.
Build Docker image or use uploaded to docker.io.
docker build . -t biolabs/jbr --platform=amd64
The user creates a number of preconfigured JRB sessions, place them in a separate <sessions_folder>
on the local
machine, and easily set up a server using publicly available Docker image biolabs/jbr
with the command:
docker run --publish=5000:5000 --volume=<sessions_folder>:/jbr_sessions --volume=<logs_folder>:/jbr_logs -d -t biolabs/jbr
Use this Issues Tracker to suggest new features or report bugs.
JetBrains Research BioLabs homepage