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CummeRbund (R-package)

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Description Content
module load bio/r_cummerbund (R-plugin only)
License Artistic-2.0
Citing Citing infos...
Links Bioconductor CummeRbund Homepage
Graphical Interface no
Dependencies R 3.2.1


1 Description/What is cummeRbund?

CummeRbund is a visualization package for Cufflinks high-throughput sequencing data. It is designed to help you navigate through the large amount of data produced from a Cuffdiff RNA-Seq differential expression analysis. The results of this analysis are typically a large number of inter-related files that are not terribly intuitive to navigate through.

CummeRbund helps promote rapid analysis of RNA-Seq data by aggregating, indexing, and allowing you easily visualize and create publication-ready figures of your RNA-Seq data while maintaining appropriate relationships between connected data points.

CummeRbund is a multifaceted suite for streamlined analysis and visualization of massively parallel RNA differential expression data sequencing data.

For more information on features please visit the CummeRBund User Guide (PDF)

2 Versions and Availability

A list of versions currently available on all bwHPC-C5-Clusters can be obtained from the

Cluster Information System CIS

On the command line interface you'll get a list of available versions by using the command module avail bio/r_cummerbund.

$ module avail bio/r_cummerbund
--------------- /opt/bwhpc/common/modulefiles ---------------
bio/r_cummerbund/2.13.1


3 License

The program CummeRbund is a free software package.
Artistic-2.0 License

4 Citing

Citation (from within R, enter citation("cummeRbund")):
Goff L, Trapnell C and Kelley D (2013). cummeRbund: Analysis, exploration, manipulation, and visualization of Cufflinks high-throughput sequencing data.. R package version 2.12.1.

5 Usage

5.1 Loading the module

  • CummeRbund is not a normal module to load for!
  • In this module you'll find only the complete installation instruction for your own $HOME environment.
  • You have to start this installtion only once for each individual user on the cluster.

5.2 R-Plugin Installation of cummeRbund

  • Again: It's only a R-plugin.

Installing the package without root access into your own $HOME folder. You have to do the following installation ONE TIME ONLY.

5.2.1 Part One: Command Prompt

Inside your $HOME folder use the following installation procedure ('$' is the command prompt and not part of the entries).
If you are a permanent user of R, modify the content of the $R_LIBS_USER environment to your own path of R plugins.

$ echo 'export R_LIBS_USER=$HOME/R' >> $HOME/.bashrc
$ export R_LIBS_USER=${HOME}/R  # your own $HOME-folder for R plugins.
$ mkdir -vp ${R_LIBS_USER} # create folder if not existing
$ cd ${R_LIBS_USER} && pwd # go to the plugin folder
$ git clone https://github.com/Bioconductor-mirror/Rsamtools.git # get Rsamtools

5.2.2 Part Two: Inside R

Start R and install the rest. Do NOT use R INSTALL... here!

 $ module load math/R/3.2.1


|R| = your installation commands inside the R system.

VERY IMPORTANT
If you see the question(s)/prompts:

 |R| Update all/some/none? [a/s/n]: 

always(!) answer with 'a' (update all) and

 |R| Would you like to use a personal library instead? (y/n):

always(!) answer with 'y' (yes)

Now start R and finish the rest of the installation

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

Only use the above installation instructions!
The complete procedure lasts about 30 minutes. So stay tuned.
You do not need to load this module again if you plan to use cummeRbund in the future.
It's included in your own set of R-plugins from now on.

6 CummeRbund-Specific Environments

  • R_LIBS_USER=${HOME}/R # your own $HOME-folder for R plugins.

Add this one to your $HOME/.bashrc for future use.
Modify the path if you are an experienced user of R and include the new plugins into your old plugin-folder (if existing).

7 Version-Specific Information

For a more detailed information specific to a specific CummeRbund version, see the information available via the module system with the command module help bio/r_cummerbund.
For a small abstract what CummeRbund is about use the command module whatis bio/r_cummerbund.
Example:

$ module whatis bio/r_cummerbund
bio/r_cummerbund     : A R package for exploration, analysis, 
  manipulation, and visualization of Cufflinks high-throughput
  RNA Sequencing data.

$ module help bio/r_cummerbund
------- Module Specific Help for 'bio/r_cummerbund/2.13.1' -------
DESCRIPTION

cummeRbund is a visualization package inside 'R' for Cufflinks 
high-throughput sequencing data.
It is designed to help you navigate through the large amount of data
produced from a Cuffdiff RNA-Seq differential expression analysis.
[...]

INSTALLATION INSTRUCTIONS 

Installing the package without root access into your own $HOME folder.
You have to do the following installation ONE TIME ONLY.

* PART ONE
  Inside your $HOME folder use the following installation
  procedure ('$' is the command prompt and not part of the entries).
  ...
[...]
 
DOCUMENTATION

* Get started, cummeRbund Homepage
   http://bioconductor.org/packages/release/bioc/html/cummeRbund.html 

* Documentation for the version of this package installed in your system.
   Start 'R' and enter:
   |R| browseVignettes("cummeRbund")
[...]

# loading the module will show this infos only:
$ module load bio/r_cummerbund
This is not a loadable standalone module. CummeRbund is a R-plugin
See installation infos by typing 'module help bio/r_cummerbund/2.13.1'