title: caOmicsV: an R package for visualizing multidimensional cancer genomic data.
abstract: BACKGROUND
  Translational genomics research in cancers, e.g., International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA), has generated large multidimensional datasets from high-throughput technologies. Data analysis at multidimensional level will greatly benefit clinical applications of genomic information in diagnosis, prognosis and therapeutics of cancers. To help, tools to effectively visualize integrated multidimensional data are important for understanding and describing the relationship between genomic variations and cancers.
  
  
  RESULTS
  We implemented the R package, caOmicsV, to provide methods under R environment to visualize multidimensional cancer genomic data in two layouts: matrix layout and combined biological network and circular layout. Both layouts support to display sample information, gene expression (e.g., RNA and miRNA), DNA methylation, DNA copy number variations, and summarized data. A set of supplemental functions are included in the caOmicsV package to help users in generation of plot data sets from multiple genomic datasets with given gene names and sample names. Default plot methods for both layouts for easy use are also implemented.
  
  
  CONCLUSIONS
  caOmicsV package provides an easy and flexible way to visualize integrated multidimensional cancer genomic data under R environment.
authors.affiliation: Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Building 37, Room 6138, 37 Convent Drive, Bethesda, MD, 20892-4265, USA.
authors.forename: Hongen
authors.initials: H
authors.lastname: Zhang
authors.affiliation: Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Building 37, Room 6138, 37 Convent Drive, Bethesda, MD, 20892-4265, USA.
authors.forename: Paul S
authors.initials: PS
authors.lastname: Meltzer
authors.affiliation: Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Building 37, Room 6138, 37 Convent Drive, Bethesda, MD, 20892-4265, USA. sdavis2@mail.nih.gov.
authors.forename: Sean R
authors.initials: SR
authors.lastname: Davis
mesh_terms: D056915:DNA Copy Number Variations; D019175:DNA Methylation; D023281:Genomics; D006801:Humans; D035683:MicroRNAs / Q000378:metabolism; D009369:Neoplasms / Q000235:genetics* / Q000473:pathology; D012333:RNA, Messenger / Q000378:metabolism; D012984:Software
chemical_list: D035683:MicroRNAs; D012333:RNA, Messenger
keywords: Genomic data visualization; Multidimensional data visualization; R package; Software