BioC 2011

Seattle, USA

2011-07-28 ~ 2011-07-29

Instructors

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

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

Morning Talks

Afternoon Labs

An Introduction to the IRanges Infrastructure Through Case Studies

Instructor: Michael Lawrence

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

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

Install command:

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

Efficient manipulation of genomic sequences in R

Instructor: Herve Pages

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

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

Install command:

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

Accessing Public Genomic Data Using Bioconductor

Instructor: Sean Davis

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

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

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

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

Install command:

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

The Bioconductor "Federation" of Annotation Packages

Instructor: Marc Carlson

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"))

Fred Hutchinson Cancer Research Center