Bioconductor
Category |
Version |
Author |
Description
Program on:
altix
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inQuiry
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pcluster
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rcluster,IOB
Category(ies): Bioinformatics
Version: 1.9 (compiled with R-2.4.0)
Author / Distributor: See http://www.bioconductor.org/
Description:
Bioconductor is an open source and open development software project for the analysis
and comprehension of genomic data.
altix: not available on altix
inQuiry: not available at inQuiry
pcluster: not available on pcluster
rcluster,IOB:Running Program | Documentation | Installation | System
Running Program:
The bioconductor libraries can be run using an R program.
Example of how to run R in a batch queue:
- create a script (called runR.sh in this example) with the following
line:
time R CMD
BATCH R_program_name
- submit this script runR.sh to a serial queue (e.g., using up to 24h of wallclock time):
rcluster>
chmod u+x runR.sh
rcluster>
bsub -q r1-24h -o out.%J -e err.%J ./runR.sh
For more information on how to run batch jobs on rcluster, please refer to
Running jobs on rcluster
Documentation:
http://www.bioconductor.org/. See also documentation on R.
Installation:
- Installed with R version 2.4.0, which is installed in
/usr/local/R-2.4.0/bin/, a directory that is
on users default path.
- Compiled with PGI compilers.
- The Bioconductor package installed consists of the following R libraries:
affy, affydata, affyio, affyPLM, annaffy, annotate,
Biobase, Biostrings, DynDoc, edd, gcrma,
genefilter, geneplotter, globaltest, GO, golubEsets, hgu95av2, KEGG, limma,
makecdfenv, marray, matchprobes, multtest, pamr, RColorBrewer,
ROC, siggenes, sma, statmod, tkWidgets, vsn, widgetTools, xtable
NOTE: ROC was compiled with a maximum length of
truth set to 100000. This value can be increased upon request.
System: 64-bit Linux
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