[BioC] Proper references for CRAN and Bioconductor

[James W. MacDonald]

Hi Greg,

Alvord, Greg (DMS) [Contr] wrote:
>             Dear List - 
> 
>  
> 
>             Please forgive a stupid but simple question.
> 
>  
> 
>             We are about to submit a paper in which the analyses were
> performed using R version 2.4.0 under Windows and Bioconductor version
> 1.9.  Part of the submission includes all the R code to reproduce all
> the results in the paper.
> 
>  
> 
>             Can anyone please tell me the most efficacious way to
> reference 
> 
>  
> 
>             (1) R version 2.4.0 , and

citation()

> 
>             (2) Bioconductor version 1.9

I don't think you can just cite the version of BioC. I think you want to 
cite the individual packages you used. Some packages have reasonable 
citations, and others just have the stock citation. You can check using 
the citation() function.

 > citation("limma")

Citing limma in publications will usually involve citing one or more of 
the methodology
papers that the software is based on as well as citing the software 
package itself. For
the methodology papers, see http://bioinf.wehi.edu.au/limma.  The 
software itself can
be cited as:

   Smyth, G. K. (2005). Limma: linear models for microarray data. In: 
'Bioinformatics
   and Computational Biology Solutions using R and Bioconductor'. R. 
Gentleman, V.
   Carey, S. Dudoit, R. Irizarry, W. Huber (eds), Springer, New York, 
pages 397--420.

A BibTeX entry for LaTeX users is

   @inbook{,
     title = {Limma: linear models for microarray data},
     author = {Gordon K Smyth},
     booktitle = {Bioinformatics and Computational Biology Solutions 
using R and Bioconductor},
     editor = {R. Gentleman, V. Carey, S. Dudoit, R. Irizarry, W. Huber},
     publisher = {Springer},
     address = {New York},
     year = {2005},
     pages = {397--420},
   }

This free open-source software implements academic research by the 
authors and
co-workers. If you use it, please support the project by citing the 
appropriate journal
articles.

Best,

Jim


> 
>  
> 
> Thanks very much in advance,
> 
>  
> 
>             Greg 
> 
>  
> 
> W. Gregory Alvord, Ph.D.
> 
> Director, Statistical Consulting Services
> 
> Computer and Statistical Services
> 
> National Cancer Institute at Frederick
> 
> Post Office Box B 
> 
> Frederick, MD 21702-1201
> 
> Phone: 301.846.5101
> 
> Facsimile: 301.846.6196
> 
> E-Mail gwa at css.ncifcrf.gov <mailto:gwa at css.ncifcrf.gov> 
> 
>  
> 
>  
> 
> 
> 	[[alternative HTML version deleted]]
> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623


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