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@ARTICLE{Ulrich:186493,
      author       = {E. Ulrich$^*$ and S. M. Pfister$^*$ and N. Jäger$^*$},
      title        = {{R}evana: a comprehensive tool for regulatory variant
                      analysis and visualization of cancer genomes.},
      journal      = {Bioinformatics},
      volume       = {39},
      number       = {1},
      issn         = {0266-7061},
      address      = {Oxford},
      publisher    = {Oxford Univ. Press},
      reportid     = {DKFZ-2022-03214},
      pages        = {btac831},
      year         = {2023},
      note         = {#EA:B062#LA:B062# / 2023 Jan 1;39(1):btac831},
      abstract     = {As non-coding driver mutations move more into the focus of
                      cancer research, a comprehensive and easy to use software
                      solution for regulatory variant analysis and data
                      visualization is highly relevant. The interpretation of
                      regulatory variants in large tumor genome cohorts requires
                      specialized analysis and visualization of multiple layers of
                      data, including for example breakpoints of structural
                      variants, enhancer elements and additional available gene
                      locus annotation, in the context of changes in gene
                      expression.We introduce a user-friendly tool, Revana
                      (REgulatory Variant ANAlysis), that can aggregate and
                      visually represent regulatory variants from cancer genomes
                      in a gene-centric manner. It requires whole genome (WGS) and
                      RNA sequencing (RNA-Seq) data of a cohort of tumor samples
                      and creates interactive HTML reports summarizing the most
                      important regulatory events.Revana is implemented in R and
                      JavaScript. It is available for download as an R package
                      under <https://github.com/KiTZ-Heidelberg/revana>. Sample
                      results can be viewed under
                      <https://github.com/KiTZ-Heidelberg/revana-demo-report> and
                      a short walkthrough is available under
                      <https://github.com/KiTZ-Heidelberg/revana-demo-data>.Supplementary
                      data are available at Bioinformatics online.},
      cin          = {B062 / HD01},
      ddc          = {570},
      cid          = {I:(DE-He78)B062-20160331 / I:(DE-He78)HD01-20160331},
      pnm          = {312 - Funktionelle und strukturelle Genomforschung
                      (POF4-312)},
      pid          = {G:(DE-HGF)POF4-312},
      typ          = {PUB:(DE-HGF)16},
      pubmed       = {pmid:36576005},
      doi          = {10.1093/bioinformatics/btac831},
      url          = {https://inrepo02.dkfz.de/record/186493},
}