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ICHEC Software

Information about software packages installed on the ICHEC systems.

Bioconductor

Versions Installed

Stokes: 2.6

Description

Bioconductor is an open source and open development software project to provide tools for the analysis and comprehension of genomic data. It is based primarily on the R programming language, but does contain contributions in other programming languages. Most Bioconductor components are distributed as R packages, which are add-on modules for R. Initially most of the Bioconductor software packages focused primarily on DNA microarray data analysis. As the project has matured, the functional scope of the software packages broadened to include the analysis of all types of genomic data, such as SAGE, sequence, or SNP data.

For version 2.6 of this package on Stokes, 389 out of the 539 individual R packages were installed. The remaining packages had compilation and library dependency issues that could be examined further upon specific request by users. Please submit a request through our Helpdesk if you'd like to use specific packages in this distribution that are missing.

License

The Bioconductor project has a commitment to full open source discipline, with distribution via a SourceForge-like platform. All contributions are expected to exist under an open source license such as Artistic 2.0, GPL2, or BSD.

Benchmarks

N/A.

Additional Notes

To use Bioconductor, load the relevant environment module, including the R module which is a prerequisite:

module load R bioconductor

Further information can be obtained from http://www.bioconductor.org/.

How to cite Bioconductor:

Gentleman R.C., Carey V.J., Bates D.M., Bolstad B., Dettling M., Dudoit S., Ellis B., Gautier L., Ge Y., Gentry J., Hornik K., Hothorn T., Huber W., Iacus S., Irizarry R., Leisch F., Li C., Maechler M., Rossini A.J., Sawitzki G., Smith C., Smyth G., Tierney L., Yang J.Y. and Zhang J. (2004)
Bioconductor: open software development for computational biology and bioinformatics.
Genome Biol. 5(10): R80.

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