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Trends in genomic data analysis with R / Bioconductor

Boston, USA

2014-07-15 ~ 2014-07-15

Instructors

  • Levi Waldron, City University of New York, Hunter College
  • Martin Morgan, Fred Hutchinson Cancer Research Center
  • Vincent Carey, Harvard Medical School
  • Mike Love, Dana-Farber Cancer Institute

Description

The Bioconductor project is a leading development and analysis environment for bioinformatics, supported by a core of dedicated programmers and a broad contributing scientific community. The project is evolving rapidly along with sequencing technologies and the quantity of available genome annotation, and this workshop provides ISMB attendees with the inside track on the most recent and upcoming trends in Bioconductor. The workshop will begin with a high-level tour of leading Bioconductor packages and capabilities across a wide variety of disciplines, then will cover current advances for 1) accessing genomic annotation data such as ENCODE and the UCSC genome browser through the AnnotationHub architecture, 2) data and algorithm element designs for integrative analysis of large genomic data and annotation that permit scalable resource utilization at run-time, and 3) analysis of RNA-seq data. The workshop features the project leader Martin Morgan, co-founders and Core member Vince Carey, Advisory Board member Levi Waldron, and post-doctoral fellow Michael Love (Rafael Irizarry lab). This workshop is intended for a wide audience and will be valuable for beginner to experienced analysts of genomic data.

Materials

Overview – Levi Waldron

  • pdf Slide presentation

Accessing Annotation Resources – Martin Morgan

  • pdf Slide presentation
  • R Basic work flows: from SYMBOL to gene model and sequence
  • R AnnotationHub work flow: evolutionarily conserved enhancer SNPs near genes on chr17

Scalable Integrative Bioinformatics with Bioconductor – Vincent Carey

  • ppt Slide presentation

Analysis of RNA-seq Data – Mike Love