Introduction to Bioconductor for High-Throughput Sequence Analysis

Seattle, USA

2014-02-27 ~ 2014-02-28

Instructors

• Sonali Arora
• Nathaniel Hayden
• Martin Morgan
• Hervé Pagès
• Marc Carlson
• Valerie Obenchain
• Dan Tenenbaum
• Paul Shannon

Description

Introduction to Bioconductor for Sequence Analysis introduces users with some R experience to Bioconductor, especially working with high-throughput sequence data. Day 1 develops core R and Bioconductor concepts for working with large and complicated data. Participants will become familiar with data classes, packages, and scripting and programming concepts that are important for common and integrated work flows in Bioconductor. Day 2 will put these skills to use for the analysis of RNAseq differential expression data, including initial quality assessment, pre-processing, differential representation, annotation, and visualization. The course involves a combination of presentations and hands-on exercises; participants should come prepared with a modern laptop with wireless internet access.

Materials

Download and install the package (containing all material) for use with R-3.1.0 / Bioconductor 2.14.

• BiocIntro_0.0.4.tar.gz

Install the course package with

source("http://bioconductor.org/biocLite.R")
dependencies <- c("Biostrings", "ShortRead", "ggplot2")
biocLite(dependencies)
install.packages("BiocIntro_0.0.3.tar.gz", repos=NULL)

Optionally, install suggested packages (used in exercises, etc) with

source("http://bioconductor.org/biocLite.R")
suggested <- c("BiocStyle", "knitr", "AnnotationHub",
    "BSgenome.Hsapiens.UCSC.hg19", "BiocParallel", "Biostrings",
    "GenomicAlignments", "GenomicFeatures", "GenomicRanges",
    "Gviz", "IRanges", "PSICQUIC", "RNAseqData.HNRNPC.bam.chr14",
    "TxDb.Hsapiens.UCSC.hg19.knownGene", "VariantAnnotation",
    "biomaRt", "knitr", "org.Hs.eg.db", "parallel", "rtracklayer")
biocLite(suggested)

Explore the material through the following documents:

Introduction

• pdf, Rnw Abstract and tentative schedule
• pdf, Rnw Slides

Working with R

• pdf, R, Rnw Slides
• pdf, R, Rnw Exercise

Sequencing work flows

• pdf, Rnw Slides

Bioconductor for Sequence Analysis

• pdf, R, Rnw Bioconductor - Slides
• pdf, R, Rnw Genomic Ranges - Slides
• pdf, R, Rnw Working with DNA Sequences
• pdf, R, Rnw Working with FASTQ, BAM, and VCF files
• pdf, R, Rnw Working with Genomic Ranges

RNA-Seq

• pdf, R, Rnw RNASeq Analysis
• Exercises: see the RNA-seq Differential Expression Lab

Annotation and visualization

• pdf, R, Rnw Slides
• pdf, R, Rnw Working with Annotations
• pdf, R, Rnw Visualization of Genomic Data