GenomeBrowse 3.0.0 – Free Genome Browser for Exploring Sequencing Pile-up

GenomeBrowse 3.0.0

:: DESCRIPTION

GenomeBrowse raises the bar on the experience of exploring and finding key insights into your genomic data. Every component has been designed and optimized to give you a user-experience beyond imagination.

::DEVELOPER

Golden Helix, Inc

:: SCREENSHOTS

GenomeBrowse

::REQUIREMENTS

  • Windows/Linux/MacOsX

:: DOWNLOAD

 GenomeBrowse

:: MORE INFORMATION

iPiG r5 – Integrating PSMs into Genome Browser Visualisations

iPiG r5

:: DESCRIPTION

iPiG targets the integration of peptide spectrum matches (PSMs) from mass spectrometry (MS) peptide identifications into genomic visualisations provided by genome browser such as the UCSC genome browser

::DEVELOPER

iPiG team

: SCREENSHOTS

iPiG

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • java

:: DOWNLOAD

  iPiG

:: MORE INFORMATION

Citation

iPiG: Integrating Peptide Spectrum Matches Into Genome Browser Visualizations
Mathias Kuhring and Bernhard Y. Renard
PLoS ONE 7(12): e50246. doi:10.1371/journal.pone.0050246

JBrowse 1.12.1 – JavaScript Genome Browser

 JBrowse 1.12.1

:: DESCRIPTION

JBrowse is a JavaScript genome browser with an emphasis on portability. JBrowse helps preserve the user’s sense of location by avoiding discontinuous transitions, instead offering smoothly animated panning, zooming, navigation, and track selection. Unlike most existing genome browsers, where the genome is rendered into images on the webserver and the role of the client is restricted to displaying those images, JBrowse distributes work between the server and client and therefore uses significantly less server overhead than previous genome browsers.

::DEVELOPER

Holmes lab at UC Berkeley

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

JBrowse

:: MORE INFORMATION

Citation:

JBrowse: a next-generation genome browser.
Skinner ME, Uzilov AV, Stein LD, Mungall CJ, Holmes IH.
Genome Res. 2009 Sep;19(9):1630-8. doi: 10.1101/gr.094607.109

Rgb 1.4.1 – Genome Browser for R

Rgb 1.4.1

:: DESCRIPTION

Rgb (R genome browser) package is dedicated to memory efficient genome browsing strategies (both in scripts and interactive sessions) using the R scripting language. It includes classes and functions to manipulate genomic tracks, and a higher level interactive genome browser.

::DEVELOPER

Sylvain Mareschal

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • R

:: DOWNLOAD

 Rgb

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Apr 21.
Rgb: a scriptable genome browser for R.
Mareschal S1, Dubois S, Lecroq T, Jardin F.

rtracklayer 1.30.4 – R interface to Genome Browsers and their Annotation Tracks

rtracklayer 1.30.4

:: DESCRIPTION

The rtracklayer package supports the integration of existing genome browsers with experimental data analyses performed in R.

:: DEVELOPER

Michael Lawrence <michafla@gene.com>, Vincent J Carey, Robert Gentleman

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac OsX/Windows
  • R package
  • BioConductor

:: DOWNLOAD

 rtracklayer

:: MORE INFORMATION

Citation

Bioinformatics. 2009 Jul 15;25(14):1841-2. doi: 10.1093/bioinformatics/btp328..
rtracklayer: an R package for interfacing with genome browsers.
Lawrence M, Gentleman R, Carey V.

RNASeqBrowser V2 – A Genome Browser for Strand Specific RNAseq Reads

RNASeqBrowser V2

:: DESCRIPTION

RNASeqBrowser is a visualization tool that incorporates and extends the functionality of the UCSC genome browser. For example, RNASeqBrowser simultaneously displays read coverage, SNPs, InDels and raw read tracks with other BED and wiggle tracks — all being dynamically built from the BAM file.

::DEVELOPER

Systems Biology of Gene Regulatory Elements

:: SCREENSHOTS

RNASeqBrowser

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  •  java

:: DOWNLOAD

  RNASeqBrowser

:: MORE INFORMATION

GeneWall Genome Browser 3.0.1 – Genome Browser for the iPad/iPhone

GeneWall Genome Browser 3.0.1

:: DESCRIPTION

GeneWall is a native genome browser for the iPad/iPhone.The genome at your fingertips (literally): Tap, scroll and pinch your way through the chromosomes, genes and genomic data.

::DEVELOPER

Wobblebase Inc

:: SCREENSHOTS

GeneWall

:: REQUIREMENTS

  •   iPhone /iPad

:: DOWNLOAD

 GeneWall Genome Browser

:: MORE INFORMATION

Genome Maps 3.0.4 – New Generation Genome Browser

Genome Maps 3.0.4

:: DESCRIPTION

Genome Maps is a genome browser that implements an innovative model of data transfer and management.

::DEVELOPER

the Computational Biology Unit, at Computational Medicine Institute at CIPF in Valencia, Spain.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • HTML5

:: DOWNLOAD

  Genome Maps

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2013 Jul;41(Web Server issue):W41-6. doi: 10.1093/nar/gkt530. Epub 2013 Jun 8.
Genome Maps, a new generation genome browser.
Medina I1, Salavert F, Sanchez R, de Maria A, Alonso R, Escobar P, Bleda M, Dopazo J.

GenomeView 2450 – Next-generation Genome Browser and Editor

GenomeView 2450

:: DESCRIPTION

GenomeView is a next-generation stand-alone genome browser and editor.It provides interactive visualization of sequences, annotation, multiple alignments, syntenic mappings, short read alignments and more. Many standard file formats are supported and new functionality can be added using a plugin system.

:DEVELOPER

Thomas Abeel, Broad Institute

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / MacOsX /  Linux
  • Java

:: DOWNLOAD

 GenomeView

:: MORE INFORMATION

Citation

GenomeView: a next-generation genome browser
Thomas Abeel; Thomas Van Parys; Yvan Saeys; James Galagan; Yves Van de Peer
Nucleic Acids Research 2011; doi: 10.1093/nar/gkr995

SMRT View 2.3.0 – Genome Browser that visualizes data generated by PacBio® Sequencing System

SMRT View 2.3.0

:: DESCRIPTION

SMRT® View is an open source Genome Browser that visualizes data generated by PacBio® Sequencing Systems.

::DEVELOPER

Pacific Biosciences of California, Inc

:: SCREENSHOTS

SMRTAnalysis

:: REQUIREMENTS

  • Linux/windows/macosx
  • Java

:: DOWNLOAD

 SMRT View

:: MORE INFORMATION