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@ARTICLE{Lohse:22185,
      author       = {Lohse, M. and Bolger, A.M. and Nagel, A. and Fernie, A.R.
                      and Lunn, J.E. and Stitt, M. and Usadel, B.},
      title        = {{R}obi{NA}: a user-friendly, integrated software solution
                      for {RNA}-{S}eq-based transcriptomics},
      journal      = {Nucleic Acids Research},
      volume       = {40},
      issn         = {0305-1048},
      address      = {Oxford},
      publisher    = {Oxford Univ. Press},
      reportid     = {PreJuSER-22185},
      pages        = {W622 - W 627},
      year         = {2012},
      note         = {Funding for open access charge: The Max Planck Society;
                      RobiNA was developed within the Plant KBBE-SAFQIM, the
                      German Ministry of Education and Research (BMBF) [project
                      0315912].},
      abstract     = {Recent rapid advances in next generation RNA sequencing
                      (RNA-Seq)-based provide researchers with unprecedentedly
                      large data sets and open new perspectives in
                      transcriptomics. Furthermore, RNA-Seq-based transcript
                      profiling can be applied to non-model and newly discovered
                      organisms because it does not require a predefined measuring
                      platform (like e.g. microarrays). However, these novel
                      technologies pose new challenges: the raw data need to be
                      rigorously quality checked and filtered prior to analysis,
                      and proper statistical methods have to be applied to extract
                      biologically relevant information. Given the sheer volume of
                      data, this is no trivial task and requires a combination of
                      considerable technical resources along with bioinformatics
                      expertise. To aid the individual researcher, we have
                      developed RobiNA as an integrated solution that consolidates
                      all steps of RNA-Seq-based differential gene-expression
                      analysis in one user-friendly cross-platform application
                      featuring a rich graphical user interface. RobiNA accepts
                      raw FastQ files, SAM/BAM alignment files and counts tables
                      as input. It supports quality checking, flexible filtering
                      and statistical analysis of differential gene expression
                      based on state-of-the art biostatistical methods developed
                      in the R/Bioconductor projects. In-line help and a
                      step-by-step manual guide users through the analysis.
                      Installer packages for Mac OS X, Windows and Linux are
                      available under the LGPL licence from
                      http://mapman.gabipd.org/web/guest/robin.},
      keywords     = {J (WoSType)},
      cin          = {IBG-2},
      ddc          = {570},
      cid          = {I:(DE-Juel1)IBG-2-20101118},
      pnm          = {Terrestrische Umwelt},
      pid          = {G:(DE-Juel1)FUEK407},
      shelfmark    = {Biochemistry $\&$ Molecular Biology},
      typ          = {PUB:(DE-HGF)16},
      pubmed       = {pmid:22684630},
      pmc          = {pmc:PMC3394330},
      UT           = {WOS:000306670900102},
      doi          = {10.1093/nar/gks540},
      url          = {https://juser.fz-juelich.de/record/22185},
}