title: Genome-wide quantitative analysis of DNA methylation from bisulfite sequencing data.
abstract: Here we present the open-source R/Bioconductor software package BEAT (BS-Seq Epimutation Analysis Toolkit). It implements all bioinformatics steps required for the quantitative high-resolution analysis of DNA methylation patterns from bisulfite sequencing data, including the detection of regional epimutation events, i.e. loss or gain of DNA methylation at CG positions relative to a reference. Using a binomial mixture model, the BEAT package aggregates methylation counts per genomic position, thereby compensating for low coverage, incomplete conversion and sequencing errors.
  
  
  METHODS
  BEAT is freely available as part of Bioconductor at www.bioconductor.org/packages/devel/bioc/html/BEAT.html. The package is distributed under the GNU Lesser General Public License 3.0.
authors.affiliation: Tresch Group, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany, AG Haaf, Institute of Human Genetics, Julius Maximilians University, 97070 Wuerzburg, Germany and Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
authors.forename: Kemal
authors.initials: K
authors.lastname: Akman
authors.affiliation: Tresch Group, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany, AG Haaf, Institute of Human Genetics, Julius Maximilians University, 97070 Wuerzburg, Germany and Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
authors.forename: Thomas
authors.initials: T
authors.lastname: Haaf
authors.affiliation: Tresch Group, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany, AG Haaf, Institute of Human Genetics, Julius Maximilians University, 97070 Wuerzburg, Germany and Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
authors.forename: Silvia
authors.initials: S
authors.lastname: Gravina
authors.affiliation: Tresch Group, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany, AG Haaf, Institute of Human Genetics, Julius Maximilians University, 97070 Wuerzburg, Germany and Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
authors.forename: Jan
authors.initials: J
authors.lastname: Vijg
authors.affiliation: Tresch Group, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany, AG Haaf, Institute of Human Genetics, Julius Maximilians University, 97070 Wuerzburg, Germany and Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
authors.forename: Achim
authors.initials: A
authors.lastname: Tresch
mesh_terms: D019175:DNA Methylation; D016678:Genome; D055106:Genome-Wide Association Study; D023281:Genomics / Q000379:methods*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D012985:Software Design; D013447:Sulfites / Q000737:chemistry*
chemical_list: D013447:Sulfites