title: rbamtools: an R interface to samtools enabling fast accumulative tabulation of splicing events over multiple RNA-seq samples.
abstract: The open source environment R isf the most widely used software to statistically explore biological data sets including sequence alignments. BAM is the de facto standard file format for sequence alignment. With rbamtools, we provide now a full spectrum of accessibility to BAM for R users such as reading, writing, extraction of subsets and plotting of alignment depth where the script syntax closely follows the SAM/BAM format. Additionally, rbamtools enables fast accumulative tabulation of splicing events over multiple BAM files.
authors.affiliation: Center for Bioinformatics and Biostatistics, BMFZ, Heinrich Heine University Düsseldorf, Institut für Virologie, and Mathematical Institute, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany.
authors.forename: Wolfgang
authors.initials: W
authors.lastname: Kaisers
authors.affiliation: Center for Bioinformatics and Biostatistics, BMFZ, Heinrich Heine University Düsseldorf, Institut für Virologie, and Mathematical Institute, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany Center for Bioinformatics and Biostatistics, BMFZ, Heinrich Heine University Düsseldorf, Institut für Virologie, and Mathematical Institute, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany.
authors.forename: Heiner
authors.initials: H
authors.lastname: Schaal
authors.affiliation: Center for Bioinformatics and Biostatistics, BMFZ, Heinrich Heine University Düsseldorf, Institut für Virologie, and Mathematical Institute, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany Center for Bioinformatics and Biostatistics, BMFZ, Heinrich Heine University Düsseldorf, Institut für Virologie, and Mathematical Institute, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany.
authors.forename: Holger
authors.initials: H
authors.lastname: Schwender
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D023281:Genomics / Q000379:methods; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D012326:RNA Splicing / Q000235:genetics*; D016415:Sequence Alignment / Q000379:methods*; D017423:Sequence Analysis, RNA / Q000379:methods*; D012984:Software