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Brown CBC's Bioconductor Workshop 1 Materials

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Goal

This workshop, 'R/Bioconductor Workshop for Genomic Data Analysis', is designed to introduce attendees to Bioconductor and a variety of its use cases; it is an intermediate-level lecture that presupposes some knowledge of R like that found in our 'Fundamentals of R' workshop. Users will apply their knowledge of basic R operations to data structures that are commonly encountered in the field of computational biology like sequence data. They will come to understand how to use R/Bioconductor to interact with common file types used in bioinformatics, receive an introduction to ontology-based analysis for deriving practical insights from the data, and then visualize the end result.

Workshop Topic Overview

The topics presented herein include the following:

  • Intro to R and Bioconductor Basic Concepts

    • Brief review of R syntax
    • Introduction to the Bioconductor repository
    • Overview of motivations, data structures, and data management for genome-scale experiments

  • Working with General Genomic Features Using Genomic Ranges

    • Introduction to Bioconductor 'ranges' package series
    • Range-oriented solutions for current experimental paradigms including RNA-seq and 450k methylation data
    • Parsing of BAM or BED formats and VCF file handling

  • Genomic Annotation with Bioconductor

    • General overview of Bioconductor annotation
    • Introduction to Ontology concepts and tools

  • Visualization of Genome-Scale Data

    • Overview of visualization tasks
    • Strategies for optimal visualization
    • Annotation-oriented visualizations

Notebook

To access a read-only version of the workshop notebooks (complete with full output), please click the above link; you will be redirected to Jupyter's NBViewer utility. Simply click the name of the notebook and it will be rendered as HTML. The notebooks can also be downloaded from this location.

Authors

Vince Carey

Contact

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Original Time and Location

Date: 2/7/2018

Location: Campus Center