VisRseq

R-based visual framework for analysis of sequencing data

Hamid Younesy, Torsten Möller, Matthew C. Lorincz, Mohammad M. Karimi, Steven J M Jones

Research output: Contribution to journalArticle

14 Citations (Scopus)

Abstract

Background: 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. Results: 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. Conclusions: 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.

Original languageEnglish
Article numberS2
JournalBMC Bioinformatics
Volume16
Issue number11
DOIs
Publication statusPublished - 13 Aug 2015
Externally publishedYes

Fingerprint

Workflow
Application programs
Sequencing
Expertise
Work Flow
Programming
Libraries
Interactivity
Graphical User Interface
Genome
Browsing
Graphical user interfaces
Repository
Usability
Genes
Framework
Vision
Datasets

Keywords

  • Interactive Visualization
  • R-project
  • Sequencing Data

ASJC Scopus subject areas

  • Structural Biology
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Applied Mathematics

Cite this

VisRseq : R-based visual framework for analysis of sequencing data. / Younesy, Hamid; Möller, Torsten; Lorincz, Matthew C.; Karimi, Mohammad M.; Jones, Steven J M.

In: BMC Bioinformatics, Vol. 16, No. 11, S2, 13.08.2015.

Research output: Contribution to journalArticle

Younesy, Hamid ; Möller, Torsten ; Lorincz, Matthew C. ; Karimi, Mohammad M. ; Jones, Steven J M. / VisRseq : R-based visual framework for analysis of sequencing data. In: BMC Bioinformatics. 2015 ; Vol. 16, No. 11.
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