Brixen-Bressanone, Italy
2014-06-22 ~ 2013-06-28
This one-week intensive course teaches current approaches in the statistical and computational analysis of large-scale experiments in biology. The course focuses on the methods for downstream analyses of high-throughput sequencing experiments including RNA sequencing (differential expression), DNA sequencing (variant calling), ChIP-Seq. Lectures also cover essentials including statistical testing, linear models, machine learning, visualisation and bioinformatic annotation. Emphasis is given to practical problem solving skills using open-source software from the Bioconductor, CRAN and other projects. The course is intended for researchers who have basic familiarity with the experimental technologies and the biology of the genome, and who are interested in developing their own, advanced data analyses using a scripting environment. The four practical sessions of the course will require simple script understanding in the computer language R. A tutorial on the required more advanced features of R will be provided, students are advised to familiarize themselves with the very basics of R beforehand. (Consider one of the many online resources or books, e.g. R-Intro from the R Project, Germán Rodríguez, R-Studio.
Morning talks
Afternoon labs
html R Intermediate R 1: accessing resources - packages, classes, methods, and efficient code. Download IntermediateR1_1.0.0.tar.gz and install as:
source("http://bioconductor.org/biocLite.R")
biocLite(c("IRanges", "GenomicRanges", "microbenchmark"))
install.packages("IntermediateR1_1.0.0.tar.gz", repos=NULL, type="source")
pdf R Intermediate R 2: scalable / performant computing. (Large files needed for some of this lab are NOT available for download). Download CSAMA2014ScalableComputingLab_0.0.1.tar.gz and install as:
source("http://bioconductor.org/biocLite.R")
biocLite(c("IRanges", "GenomicRanges", "Rsamtools", "ShortRead",
"rtracklayer", "GenomicAlignments", "GEOquery", "microbenchmark",
"BiocParallel", "ggbio", "Biobase", "GenomicFiles"))
install.packages("CSAMA2014ScalableComputingLab_0.0.1.tar.gz",
repos=NULL, type="source")
Morning talks
Afternoon labs
Morning talks
Afternoon labs
Morning talks
Afternoon labs
Morning talks
Afternoon labs
Packages »
Bioconductor's stable, semi-annual release:
Bioconductor is also available viaDocker Images and for use in the AnVIL.
Documentation »
Bioconductor
R / CRAN packages and documentation