User:Jarle Pahr/Bioconductor
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
Workflows: http://www.bioconductor.org/help/workflows/
- HTS: http://www.bioconductor.org/help/workflows/high-throughput-sequencing/
- Flow cytometry: http://www.bioconductor.org/help/workflows/highthroughputassays/
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.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
Annotate
