To be presented during useR! 2014.
Goals
- Gain overall familiarity with Bioconductor packages for high-throughput sequence analysis, including Bioconductor vignettes and classes.
- Obtain experience running bioninformatic work flows for data quality assessment, RNA-seq differential expression, and manipulating variant call format files
- Appreciate the importance of ranges and range-based manipulation for modern genomic analysis
- Learn 'best practices' for working with large data
- Key packages: Biostrings, ShortRead, GenomicRanges, GenomicAlignments, DESeq2, and VariantAnnotation.
Outline
- Introduction to Bioconductor -- packages and classes
- Short work flows
- Exploring sequences and alignments
- RNA-seq: a high-level tour
- Annotating variants
Prerequisites
The workshop assumes an intermediate level of familiarity with R, and basic understanding of biological and technological aspects of high-throughput sequence analysis. Participants should come prepared with a modern wireless-enabled laptop and web browser installed. (Please have Firefox, Chrome, or Safari installed, as RStudio Server does not work with Internet Explorer.)
Intended Audience
This workshop is for professional bioinformaticians and statisticians intending to use R / Bioconductor for analysis and comprehension of high-throughput sequence data.