title: 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.
  
  
  METHODS
  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.
authors.affiliation: Institut Curie, 26 rue d'Ulm, F-75248 Paris, INSERM U900, F-75248 Paris, France. joern.toedling@curie.fr
authors.forename: Joern
authors.initials: J
authors.lastname: Toedling
authors.forename: Constance
authors.initials: C
authors.lastname: Ciaudo
authors.forename: Olivier
authors.initials: O
authors.lastname: Voinnet
authors.forename: Edith
authors.initials: E
authors.lastname: Heard
authors.forename: Emmanuel
authors.initials: E
authors.lastname: Barillot
mesh_terms: D030541:Databases, Genetic; D016678:Genome; D023281:Genomics / Q000379:methods*; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods; D016415:Sequence Alignment / Q000379:methods*; D012984:Software; D014584:User-Computer Interface