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- Computational Statistics for Genome Biology (CSAMA)
Computational Statistics for Genome Biology (CSAMA)
Brixen-Bressanone, Italy
2013-06-24 ~ 2013-06-28
Instructors
- Martin Morgan, Fred Hutchinson Cancer Research Center (USA)
- Robert Gentleman, Genentech (USA)
- Vincent J. Carey, Channing Laboratory, Harvard Medical School (USA)
- Wolfgang Huber, European Molecular Biology Laboratory (DE)
- Simon Anders, European Molecular Biology Laboratory (DE)
- Mark Robinson, Institute of Molecular Life Sciences, University of Zurich (CH)
- Laurent Gatto, University of Cambridge (UK)
Description
This one-week intensive course teaches current approaches in the statistical and computational analysis of large-scale experiments in biology. The course focus on the methods for downstream analysis of high-throughput sequencing experiments, including DNA sequencing (variant calling), RNA sequencing (differential expression), QTL analysis, epigenetics. Lectures also cover essentials including statistical testing, machine learning, visualisation and bioinformatic metadata integration. The course is intended for researchers who have a basic familiarity with the experimental technologies and the biology of the genome. The four practical sessions of the course will require simple programming in the language R; introductory and advanced language tutorials will be provided.
Materials
Monday
Morning
130624-brixen-microarrays-huber.key
130624-brixen-microarrays-huber.pdf
130624-gentleman-statistics-intro.pdf
morgan-r-bioconductor-intro.pdf
Afternoon
For Monday / Friday labs, download Morgan2013_1.0.1.tar.gz and install as follows:
biocLite(c("Biostrings", "ShortRead", "Rsamtools",
"GenomicRanges", "rtracklayer", "RNAseqData.HNRNPC.bam.chr14",
"org.Hs.eg.db", "BSgenome.Hsapiens.UCSC.hg19",
"TxDb.Hsapiens.UCSC.hg19.knownGene", "Homo.sapiens",
"TxDb.Dmelanogaster.UCSC.dm3.ensGene", "GO.db", "MotifDb",
"seqnames.db", "SNPlocs.Hsapiens.dbSNP.20120608",
"GenomicFeatures", "biomaRt", "AnnotationHub",
"VariantAnnotation", "ensemblVEP", "VariantTools", "gmapR",
"LungCancerLines", "Gviz", "shiny", "parallel", "lattice",
"edgeR"))
install.packages("Morgan2013_1.0.1.tar.gz", repos=NULL, type="source")
sequences-reads-ranges-alignments.pdf
Tuesday
Morning
morgan-sequences-reads-ranges-alignments-suppl.txt
morgan-sequences-reads-ranges-alignments.pdf
Afternoon
Wednesday
Morning
130626-brixen-machinelearn-huber.key
130626-brixen-machinelearn-huber.pdf
Thursday
Morning
130627-multtestindepfilt-huber.key
130627-multtestindepfilt-huber.pdf
Afternoon
Friday
Morning
130628-brixen-imagephenotyping-huber.pdf