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

Anders__Alignment_Basics.odp

Anders__Alignment_Basics.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")

A1_SequenceAnalysis.R

A2_ReadsAndStrings.R

A3_AlignmentsAndRanges.R

A4_LargeData.R

BigData.zip

Data/data.csv

R-Basics.R

R-Basics.pdf

README

RefCards/Rrefcard.pdf

RefCards/Short-refcard.pdf

protocol/protocol.pdf

sequences-reads-ranges-alignments.pdf

Tuesday

Morning

Anders__DESeq_DEXSeq.pdf

brixvis2013.Rnw

bvis.bib

geneSeg.pdf

karchHilb.pdf

morgan-sequences-reads-ranges-alignments-suppl.txt

morgan-sequences-reads-ranges-alignments.pdf

vislec.pdf

Afternoon

DESeq2_parathyroid.R

DESeq2_parathyroid.Rnw

DESeq2_parathyroid.pdf

DESeq_protocol.pdf

library.bib

localUcscTable.csv

Wednesday

Morning

130626-brixen-machinelearn-huber.key

130626-brixen-machinelearn-huber.pdf

Epigenomics_Lecture1.pdf

Epigenomics_Lecture2.pdf

Thursday

Morning

130627-multtestindepfilt-huber.key

130627-multtestindepfilt-huber.pdf

integr.pdf

morgan-annotation.pdf

morgan-big-data.pdf

Afternoon

DEXSeq.R

DEXSeq.pdf

anno.Rdata

chipseq_thurs_pm.R

chipseq_thurs_pm.pdf

d.Rdata

expr.Rdata

methGR.Rdata

Friday

Morning

130628-brixen-imagephenotyping-huber.pdf

GSEA2011.pdf

RGCSAMA.pdf

morgan-pwms.pdf

reproEmerg.pdf

Afternoon

D1_GeneAnnotations.R

D2_GenomicAnnotations.R

D3_Visualization.R

D4_CalledVariants.R

D5_StructuralVariants.R

D6_RegulatoryVariants.R

Morgan2013_0.9.0.tar.gz

QuickPackage.pdf

QuickPackage_1.0.tar.gz

R-programming.R

R-programming.pdf

README

S4-tutorial.R

S4-tutorial.pdf

annotation-visualization-variants.pdf

src/parallel.R

src/parallel_bioc.R

src/parallel_export_sympols.R