VisRseq: R-based visual framework for analysis of sequencing data

BMC Bioinformatics
Hamid YounesySteven Jm Jones

Abstract

Several tools have been developed to enable biologists to perform initial browsing and exploration of sequencing data. However the computational tool set for further analyses often requires significant computational expertise to use and many of the biologists with the knowledge needed to interpret these data must rely on programming experts. We present VisRseq, a framework for analysis of sequencing datasets that provides a computationally rich and accessible framework for integrative and interactive analyses without requiring programming expertise. We achieve this aim by providing R apps, which offer a semi-auto generated and unified graphical user interface for computational packages in R and repositories such as Bioconductor. To address the interactivity limitation inherent in R libraries, our framework includes several native apps that provide exploration and brushing operations as well as an integrated genome browser. The apps can be chained together to create more powerful analysis workflows. To validate the usability of VisRseq for analysis of sequencing data, we present two case studies performed by our collaborators and report their workflow and insights.

References

Sep 15, 1998·Human Molecular Genetics·I M Morison, A E Reeve
Jun 5, 2002·Genome Research·W James KentDavid Haussler
Aug 7, 2004·Bioinformatics·James M Wettenhall, Gordon K Smyth
Oct 6, 2004·Genome Biology·Robert C GentlemanJianhua Zhang
Feb 4, 2006·Bioinformatics·James M WettenhallGordon K Smyth
Jul 3, 2007·Nature·Tarjei S MikkelsenBradley E Bernstein
Jun 3, 2008·Nature Methods·Ali MortazaviBarbara Wold
Nov 4, 2008·Nature Biotechnology·Hongkai JiWing H Wong
Jun 10, 2009·Bioinformatics·Heng LiUNKNOWN 1000 Genome Project Data Processing Subgroup
Oct 17, 2009·IEEE Transactions on Visualization and Computer Graphics·Miriah MeyerHanspeter Pfister
Oct 29, 2010·Genome Biology·Simon Anders, Wolfgang Huber
Dec 24, 2010·Nucleic Acids Research·Tao YeLaszlo Tora
Dec 25, 2010·Genome Biology·Geir K SandveEivind Hovig
Jan 12, 2011·Nature Biotechnology·James T RobinsonJill P Mesirov
Aug 24, 2011·Genome Biology·Tao LiuX Shirley Liu
Oct 29, 2011·IEEE Transactions on Visualization and Computer Graphics·Michael BostockJeffrey Heer
Oct 5, 2012·Genome Biology·Konstantin HalachevChristoph Bock
Feb 26, 2013·Bioinformatics·John GómezRafael C Jiménez
Apr 15, 2014·Bioinformatics·Hamid YounesySteven J M Jones
Aug 5, 2014·Nature Methods·Florin ChelaruHéctor Corrada Bravo
Dec 1, 2012·IEEE Transactions on Visualization and Computer Graphics·M SedlmairT Munzner

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Citations

Jun 15, 2016·The Journal of Experimental Medicine·Frann AntignanoColby Zaph
Aug 25, 2016·Database : the Journal of Biological Databases and Curation·Juliane FluckManuel Peitsch
Dec 25, 2016·Briefings in Bioinformatics·Yifeng LiAlioune Ngom
Sep 4, 2015·BMC Bioinformatics·Jan AertsDaniel Weiskopf
Feb 15, 2019·PLoS Computational Biology·Brandon MonierQin Ma
Nov 5, 2019·The Journal of Immunology : Official Journal of the American Association of Immunologists·Bernard C LoKelly M McNagny
Dec 12, 2019·The Journal of Pharmacology and Experimental Therapeutics·Violeta Balbas-MartinezIñaki F Troconiz
Dec 11, 2020·BMC Bioinformatics·Federico MariniHarald Binder
Jan 25, 2020·Cell Stem Cell·Hesham SolimanFabio M V Rossi
Jul 1, 2021·Epigenetics & Chromatin·Bradley P Balaton, Carolyn J Brown

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Methods Mentioned

BETA
nucleic acid sequencing
RNA-seq
MDS
ChIP-seq

Software Mentioned

Swing
Rattle
seqMINER
Genome Browser
Polaris
CisGenome
MDS
Tcl
Genome browsers
BAM

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