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


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2015-12

AUTHORS

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

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. More... »

PAGES

s2

Identifiers

URI

http://scigraph.springernature.com/pub.10.1186/1471-2105-16-s11-s2

DOI

http://dx.doi.org/10.1186/1471-2105-16-s11-s2

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1009796924

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/26328469


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Download the RDF metadata as:  json-ld nt turtle xml License info

HOW TO GET THIS DATA PROGRAMMATICALLY:

JSON-LD is a popular format for linked data which is fully compatible with JSON.

curl -H 'Accept: application/ld+json' 'https://scigraph.springernature.com/pub.10.1186/1471-2105-16-s11-s2'

N-Triples is a line-based linked data format ideal for batch operations.

curl -H 'Accept: application/n-triples' 'https://scigraph.springernature.com/pub.10.1186/1471-2105-16-s11-s2'

Turtle is a human-readable linked data format.

curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1186/1471-2105-16-s11-s2'

RDF/XML is a standard XML format for linked data.

curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1186/1471-2105-16-s11-s2'


 

This table displays all metadata directly associated to this object as RDF triples.

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324 schema:name Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
325 Department of Medical Genetics, The University of British Columbia, Vancouver, British Columbia, Canada
326 Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
327 rdf:type schema:Organization
 




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