Question: Proper references for CRAN and Bioconductor
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gravatar for Alvord, Greg DMS [Contr]
12.8 years ago by
Alvord, Greg DMS [Contr]160 wrote:
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ADD COMMENTlink modified 12.8 years ago by James W. MacDonald52k • written 12.8 years ago by Alvord, Greg DMS [Contr]160
Answer: Proper references for CRAN and Bioconductor
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gravatar for James W. MacDonald
12.8 years ago by
United States
James W. MacDonald52k wrote:
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]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- 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 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.
ADD COMMENTlink written 12.8 years ago by James W. MacDonald52k
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