Wednesday, 21 December 2011

Hilbertvis installation in R (no admin rights required!)

Playing around with
HilbertVis: Visualization of genomic data with the Hilbert curve

HilbertVis - Bioconductor

Trying out an idea to use Hilbert Curves as a method to visually inspect WGS mapped bams for regions of low coverage or unequal coverage across samples.

It has a standalone GUI version that requires gtk+ packages that may not be avail on all systems.

The cool thing is that it can be installed locally within your user directory with a few simple commands

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> source("")
> biocLite("HilbertVis")

Using R version 2.10.0, biocinstall version 2.5.11.
Installing Bioconductor version 2.5 packages:
[1] "HilbertVis"
Please wait...
Warning in install.packages(pkgs = pkgs, repos = repos, ...) :
  argument 'lib' is missing: using '/usr/lib64/R/library'
Warning in install.packages(pkgs = pkgs, repos = repos, ...) :
  'lib = "/usr/lib64/R/library"' is not writable
Would you like to create a personal library
to install packages into?  (y/n)

No comments:

Post a Comment

Datanami, Woe be me