BioC 2011

Seattle, USA

2011-07-28 ~ 2011-07-29

Instructors

• Stephen Lincoln
• Henrik Bengtsson
• Thomas Wu
• Gordon Smyth
• John Marioni
• Raphael Gottardo
• Jeffrey Leek
• Peter J Park
• Michael Lawrence
• Arnaud Droit
• Eloi Mercier
• Paul Shannon
• Herve Pages
• Martin Morgan
• Wolfgang Huber
• Sean Davis
• Greg Finak
• Lihua Julie Zhu
• Peter Haverty
• Vince Carey
• Marc Carlson

Description

This conference highlights current developments within and beyond Bioconductor, an international open source and open development software project for the analysis and comprehension of high-throughput genomic data.

Materials

• Download and Install R

  • R-2.14.for Windows
  • R-2.14 for MacOSX (see installation instructions here)
  • R-2.14 for Linux

Linux (Ubuntu) people may want to make sure the following packages are installed before building R from source:

• libX11-devel
• libxml-dev
• libcurl3
• libcurl3-dev

Morning Talks

• Analysis of thousands of complete human genome sequences- Stephen Lincoln, Complete Genomics.
• Single tumor-normal pair parent-specific copy number analysis - Henrik Bengtsson, Biostatistics, University of California, San Francisco.
• Analysis of multi-factor RNA-Seq experiments with respect to biologicalvariation- Gordon Smyth, Walter and Eliza Hall Institute of Medical Research.

Afternoon Labs

An Introduction to the IRanges Infrastructure Through Case Studies

Instructor: Michael Lawrence

• Slides
• R script

Install command:

source("http://bioconductor.org/BioC2011.R"); pkgInstall(c("rtracklayer", "Biostrings", "chipseq", "VariantAnnotation", "ShortRead", "TxDb.Mmusculus.UCSC.mm9.knownGene", "TxDb.Scerevisiae.UCSC.sacCer2.ensGene", "BSgenome.Scerevisiae.UCSC.sacCer2", "leeBamViews"))

A Bioconductor pipeline for the analyis of ChIP-Seq experiments

Instructor: Eloi Mercier and Arnaud Droit

• Slides

Install command:

source("http://bioconductor.org/BioC2011.R"); pkgInstall(c("PICS", "rGADEM", "MotIV", "rtracklayer", "bitops","GenomeGraphs", "ChIPpeakAnno", "seqLogo", "Biostrings", "GenomicFeatures", "BSgenome.Hsapiens.UCSC.hg17", "BSgenome.Hsapiens.UCSC.hg18", "ChipSeq"))

RCytoscape: tools for molecular cartography

Instructor: Paul Shannon

• Demo code

Install command:

source("http://bioconductor.org/BioC2011.R"); pkgInstall(c("RCytoscape", "XMLRPC", "graph", "rcyTutorial"))

Efficient manipulation of genomic sequences in R

Instructor: Herve Pages

• Biostrings BSgenome Overview
• Biostrings lab exercises
• Biostrings lab solutions

Install command:

source("http://bioconductor.org/BioC2011.R"); pkgInstall(c("Biostrings", "BSgenome", "GenomicFeatures", "hgu95av2probe", "BSgenome.Celegans.UCSC.ce2", "BSgenome.Scerevisiae.UCSC.sacCer2", "BSgenome.Hsapiens.UCSC.hg19", "SNPlocs.Hsapiens.dbSNP.20101109", "TxDb.Hsapiens.UCSC.hg19.knownGene", "TxDb.Scerevisiae.UCSC.sacCer2.ensGene"))

Rsamtools for exploration and initial analysis of aligned sequences

Instructor: Martin Morgan

• CountAndMeasure lab
• CountAndMeasure lab solutions

Install command:

source("http://bioconductor.org/BioC2011.R"); pkgInstall(c("Rsamtools", "leeBamViews", "org.Sc.sgd.db", "TxDb.Scerevisiae.UCSC.sacCer2.ensGene", "BSgenome.Scerevisiae.UCSC.sacCer2"))

Differential expression analysis for sequence count data with DESeq

Instructor: Wolfgang Huber

• Slides
• DESeq vignette
• DEXSeq vignette

Install command:

source("http://bioconductor.org/BioC2011.R"); pkgInstall(c("DESeq", "DEXSeq", "pasilla"))

Accessing Public Genomic Data Using Bioconductor

Instructor: Sean Davis

• Overview talk
• Vignette
• R code

Install command:

source("http://bioconductor.org/BioC2011.R"); pkgInstall(c("SRAdb", "GEOquery", "GEOmetadb", "ArrayExpress", "limma", "affy", "ShortRead"))

Computational Analysis of Flow Cytometry Data using Bioconductor

Instructor: Greg Finak

• Basic Flow Slides

Install command:

source("http://bioconductor.org/BioC2011.R"); pkgInstall(c("flowCore", "flowViz", "flowStats", "flowWorkspace", "Rgraphviz", "XML", "graph", "BasicFlowWorkshop"))

ChIPpeakAnno: A Bioconductor package to annotate ChIP-seq and ChIP-chip data

Instructor: Lihua Julie Zhu

• Slides
• R script

Install command:

source("http://bioconductor.org/BioC2011.R"); pkgInstall(c("ChIPpeakAnno", "biomaRt", "multtest", "IRanges", "Biostrings", "BSgenome", "BSgenome.Ecoli.NCBI.20080805", "GO.db", "org.Hs.eg.db", "limma", "gplots"))

DNA Copy Number, Allelic Imbalance, and Big Data on the Genome

Instructor: Peter Haverty

• genoset.pdf

Install command:

source("http://bioconductor.org/BioC2011.R"); pkgInstall(c("genoset", "multicore", "IRanges", "Biobase", "DNAcopy"))

Genetics of gene expression: data structures, algorithms, inference

Instructor: Vince Carey

• careyGGtutslides.pdf
• PracticalConsiderations.pdf
• extras.pdf

Install command:

source("http://bioconductor.org/BioC2011.R"); pkgInstall(c("GGtools", "ggtut", "GenomicFeatures", "Rsamtools", "ff"))

The Bioconductor “Federation” of Annotation Packages

Instructor: Marc Carlson

• Annotation Slides
• Annotation Exercise
• Annotation Solutions

Install command:

source("http://bioconductor.org/BioC2011.R"); pkgInstall(c("AnnotationDbi", "DBI", "RSQLite", "biomaRt", "ShortRead", "GenomicFeatures","GenomicFeatures", "GO.db", "KEGG.db", "human.db0", "hgu95av2.db", "hgu95av2cdf","hgu95av2probe", "org.Hs.eg.db", "org.Mm.eg.db", "TxDb.Hsapiens.UCSC.hg19.knownGene", "Annotations", "targetscan.Hs.eg.db"))