User:Jarle Pahr/Bioconductor

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Notes on the Bioconductor project (http://www.bioconductor.org/):

Bioconductor is a collection of packages for R. According to the official description, "Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data." Stable releases are made twice a year.

http://www.sbforum.org/cmsimages/presentations/BioC.pdf

http://www.homolog.us/blogs/blog/2011/11/22/rbioconductor/

To install Bioconductor, use the following commands in R:

msource("http://bioconductor.org/biocLite.R")
biocLite()

http://en.wikipedia.org/wiki/Bioconductor

http://manuals.bioinformatics.ucr.edu/home/ht-seq/

http://rss.acs.unt.edu/Rdoc/library/Biobase/doc/Bioconductor.pdf


http://www.youtube.com/watch?v=J5h5WxOn3Gw


BOL R and Bioconductor group: http://bioinformaticsonline.com/groups/profile/93/r-and-bioconductor


http://manuals.bioinformatics.ucr.edu/home/R_BioCondManual


http://www.mikromatrise.no/files/resourcesmodule/@random45250567733de/1261474815_R_and_Bioconductor_sn.pdf

Workflows: http://www.bioconductor.org/help/workflows/

Using Bioconductor to Analyze your 23andme Data: http://vincebuffalo.com/2012/03/12/23andme-gwascat.html

Training material

http://evomics.org/workshops/advanced-topics/bioconductor/

http://www.bioconductor.org/help/course-materials/2013/

http://www.bioconductor.org/help/course-materials/2013/SeattleMay2013/

http://www.bioconductor.org/help/course-materials/2013/useR2013/

http://www.ub.edu/stat/docencia/bioinformatica/microarrays/ADM/slides/T2_Bioconductor/1_BioconductorOverview-Short.pdf

http://www.bioconductor.org/help/course-materials/2012/SeattleMay2012/Bioconductor-tutorial.pdf


Bioconductor basics tutorial: http://www.bioconductor.org/help/course-materials/2002/Summer02Course/Labs/basics.pdf

Packages

For a full list of software packages, see http://www.bioconductor.org/packages/release/bioc/

For a full list of all packages, see www.bioconductor.org/packages/release/BiocViews.html


EdgeR: http://www.bioconductor.org/packages/2.12/bioc/html/edgeR.html

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