title: cgmisc: enhanced genome-wide association analyses and visualization.
abstract: High-throughput genotyping and sequencing technologies facilitate studies of complex genetic traits and provide new research opportunities. The increasing popularity of genome-wide association studies (GWAS) leads to the discovery of new associated loci and a better understanding of the genetic architecture underlying not only diseases, but also other monogenic and complex phenotypes. Several softwares are available for performing GWAS analyses, R environment being one of them.
  
  
  RESULTS
  We present cgmisc, an R package that enables enhanced data analysis and visualization of results from GWAS. The package contains several utilities and modules that complement and enhance the functionality of the existing software. It also provides several tools for advanced visualization of genomic data and utilizes the power of the R language to aid in preparation of publication-quality figures. Some of the package functions are specific for the domestic dog (Canis familiaris) data.
  
  
  METHODS
  The package is operating system-independent and is available from: https://github.com/cgmisc-team/cgmisc
  
  
  BACKGROUND
  marcin.kierczak@imbim.uu.se.
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden, Computational Genetics Section, Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden and.
authors.forename: Marcin
authors.initials: M
authors.lastname: Kierczak
authors.affiliation: Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.
authors.forename: Jagoda
authors.initials: J
authors.lastname: Jabłońska
authors.affiliation: Computational Genetics Section, Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden and.
authors.forename: Simon K G
authors.initials: SK
authors.lastname: Forsberg
authors.affiliation: Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.
authors.forename: Matteo
authors.initials: M
authors.lastname: Bianchi
authors.affiliation: Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.
authors.forename: Katarina
authors.initials: K
authors.lastname: Tengvall
authors.affiliation: Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden, Computational Genetics Section, Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden and.
authors.forename: Mats
authors.initials: M
authors.lastname: Pettersson
authors.affiliation: Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.
authors.forename: Veronika
authors.initials: V
authors.lastname: Scholz
authors.affiliation: Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.
authors.forename: Jennifer R S
authors.initials: JR
authors.lastname: Meadows
authors.affiliation: Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.
authors.forename: Patric
authors.initials: P
authors.lastname: Jern
authors.affiliation: Computational Genetics Section, Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden and.
authors.forename: Örjan
authors.initials: Ö
authors.lastname: Carlborg
authors.affiliation: Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden, Broad Institute of MIT and Harvard, Boston, MA, USA.
authors.forename: Kerstin
authors.initials: K
authors.lastname: Lindblad-Toh
mesh_terms: D000818:Animals; D003196:Computer Graphics; D004285:Dogs; D055106:Genome-Wide Association Study / Q000379:methods*; D023281:Genomics / Q000379:methods*; D005838:Genotype; D006801:Humans; D019656:Loss of Heterozygosity; D010641:Phenotype; D012984:Software