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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
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"))