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- High throughput sequence analysis with R and Bioconductor
High throughput sequence analysis with R and Bioconductor
Warwick, UK
2011-08-16 ~ 2011-08-16
Instructors
- Martin Morgan
- Herve Pages
Description
This tutorial introduces R users to the Bioconductor project, a collection of more than 400 packages for the analysis and comprehension of high-throughput genetic data. The tutorial highlights flexible facilities for the analysis of DNA sequence data.
Materials
Welcome!
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To prepare for this workshop, please install R version 2.13.1.
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Exercises require additional packages. Install these by starting an R session and entering (e.g., cut-and-paste from below)
source("http://bioconductor.org/biocLite.R") biocLite(c("GenomicFeatures", "ShortRead", "edgeR", "org.Dm.eg.db", "BSgenome.Dmelanogaster.UCSC.dm3"))
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The workshop uses moderately sized data; your laptop (Mac, Windows, or Linux) should have 2 Gb or more of memory and ample disk space.
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If using Linux or MacOS, download the Source package and install with
install.packages("useR2011_0.1.0.tar.gz", repos=NULL, type="source")
On windows, download the Windows package and install with
install.packages("useR2011_0.1.0.tar.gz", repos=NULL)
In either case, the first argument should be the path to the file that you downloaded!
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Once installed, load the library and read the extensive vignette
library(useR2011) browseVignettes("useR2011")
the package contains an extensive vignette (PDF) and R scripts for each chapter.
If you have questions, please do not hesitate to contact me, mtmorgan at fhcrc dot org.