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Girafe--an R/Bioconductor package for functional exploration of aligned next-generation sequencing reads.

ABSTRACT: The R/Bioconductor package girafe facilitates the functional exploration of alignments of sequence reads from next-generation sequencing data to a genome. It allows users to investigate the genomic intervals together with the aligned reads and to work with, visualise and export these intervals. Moreover, the package operates within and extends the ever-growing Bioconductor framework and thus enables users to leverage a multitude of methods for their data in order to answer specific research questions.The R package girafe is available from the Bioconductor web site: http://www.bioconductor.org/packages/release/bioc/html/girafe.html. An extensive vignette and the Bioconductor mailing lists provide additional documentation and help for using the package.

SUBMITTER: Toedling J

PROVIDER: S-EPMC2971573 | biostudies-literature | 2010 Nov

REPOSITORIES: biostudies-literature

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Girafe--an R/Bioconductor package for functional exploration of aligned next-generation sequencing reads.

Toedling Joern J Ciaudo Constance C Voinnet Olivier O Heard Edith E Barillot Emmanuel E

Bioinformatics (Oxford, England) 20100921 22

<h4>Unlabelled</h4>The R/Bioconductor package girafe facilitates the functional exploration of alignments of sequence reads from next-generation sequencing data to a genome. It allows users to investigate the genomic intervals together with the aligned reads and to work with, visualise and export these intervals. Moreover, the package operates within and extends the ever-growing Bioconductor framework and thus enables users to leverage a multitude of methods for their data in order to answer spe ...[more]

PMID: 20861030

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PING 2.0: An R/Bioconductor package for nucleosome positioning using next-generation sequencing data

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