Bioconductor

From CLAB

Bioconductor is an open source and open development software project for the analysis and comprehension of genomic data.

Bioconductor appears to be written using C++, fortran, and R. The C++ and Fortran components are written using those languages for performance.

1 Installation
- 1.1 Via apt-get?
- 1.2 Via R?
2 Installed Packages

[edit] Installation

Dan and I have been attempting to get BioConductor installed on klab today. These are our trials and tribulations. --Jhannah 14:28, 1 February 2008 (CST)

Admin manual: http://cran.r-project.org/doc/manuals/R-admin.html

[edit] Via apt-get?

http://bioinformaticsonline.co.uk/2007/03/30/installing_r_bioconductor_on_ubuntu_linux

# apt-get install r-bioc-repostools
Reading package lists... Done
Building dependency tree
Reading state information... Done
E: Couldn't find package r-bioc-repostools

[edit] Via R?

as root, inside R:

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

This has failed twice... see these logs:

/tmp/errors
/tmp/errors2

I got past "errors" to "errors2" by ln -s gcc gcc-4.2 which I then deleted, since that's evil. :) --Jhannah 14:31, 1 February 2008 (CST)

[edit] Installed Packages

[edit] Default packages

affy, affydata, affyPLM, annaffy, annotate, Biobase, Biostrings, DynDoc, gcrma, genefilter, geneplotter, hgu95av2, limma, marray, matchprobes, multtest, ROC, vsn, xtable, affyQCReport