useR2013!: High-throughput sequence analysis with R and Bioconductor

DNA sequence analysis generates large volumes of data presenting challenging bioinformatic and statistical problems. This tutorial introduces Bioconductor packages and work ows for the analysis of sequence data. We learn about approaches for eciently manipulating sequences and alignments, and introduce common work ows and the unique statistical challenges associated with ‘RNA-seq’, ‘ChIP-seq‘ and variant annotation experiments. The emphasis is on exploratory analysis, and the analysis of designed experiments. The workshop assumes an intermediate level of familiarity with R, and basic understanding of biological and technological aspects of highthroughput sequence analysis. The workshop emphasizes orientation within the Bioconductor milieu; we will touch on the Biostrings, ShortRead, GenomicRanges, edgeR, and DiBind , and VariantAnnotation packages, with short exercises to illustrate the functionality of each package. Participants should come prepared with a modern laptop with current R installed.