Seattle, USA
2011-07-28 ~ 2011-07-29
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.
Download and Install R
Linux (Ubuntu) people may want to make sure the following packages are installed before building R from source:
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"))
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"))
Instructor: Paul Shannon
Install command:
source("http://bioconductor.org/BioC2011.R"); pkgInstall(c("RCytoscape", "XMLRPC", "graph", "rcyTutorial"))
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"))
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"))
Instructor: Wolfgang Huber
Install command:
source("http://bioconductor.org/BioC2011.R"); pkgInstall(c("DESeq", "DEXSeq", "pasilla"))
Instructor: Sean Davis
Install command:
source("http://bioconductor.org/BioC2011.R"); pkgInstall(c("SRAdb", "GEOquery", "GEOmetadb", "ArrayExpress", "limma", "affy", "ShortRead"))
Instructor: Greg Finak
Install command:
source("http://bioconductor.org/BioC2011.R"); pkgInstall(c("flowCore", "flowViz", "flowStats", "flowWorkspace", "Rgraphviz", "XML", "graph", "BasicFlowWorkshop"))
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"))
Instructor: Peter Haverty
Install command:
source("http://bioconductor.org/BioC2011.R"); pkgInstall(c("genoset", "multicore", "IRanges", "Biobase", "DNAcopy"))
Instructor: Vince Carey
Install command:
source("http://bioconductor.org/BioC2011.R"); pkgInstall(c("GGtools", "ggtut", "GenomicFeatures", "Rsamtools", "ff"))
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"))
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