Any package for time course microarray data analysis?
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affy snp ▴ 640
@affy-snp-2480
Last seen 7.2 years ago
Dear list, Hi! I am wondering whether you can suggest me some R packages designed for analyzing time course microarray data. Thanks a lot! Alex [[alternative HTML version deleted]]
Microarray Microarray • 596 views
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@steve-lianoglou-2771
Last seen 12 hours ago
United States
Hi, > Hi! I am wondering whether you can suggest me some R packages > designed for analyzing time course microarray data. Yes, there appear to be several. Go to the bioconductor packages page: http://www.bioconductor.org/packages/release/bioc/ And search in that page for the word "time". I see at least three packages there: * maSigPro * Mfuzz * timecourse There may be more ... I haven't used any of them, so I really can't say too much more about it. HTH, -steve -- Steve Lianoglou Graduate Student: Physiology, Biophysics and Systems Biology Weill Medical College of Cornell University http://cbio.mskcc.org/~lianos
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Hi Steve You can make use of the Bioconductor task views to locate specific packages for analyzing time course micro array data. The bioconductor task views can be found at http://bioconductor.org/packages/release/BiocViews.html The views provided by biocViews integrate the software, annotation data and experiment data repositories provided by Bioconductor. Basically the biocViews field in the Description file of each package determines the views under which it appears in. For packages that deal with time course stuff please take a look at the TimeCourse subview under statistics. http://bioconductor.org/packages/release/TimeCourse.html Nishant Steve Lianoglou wrote: > Hi, > >> Hi! I am wondering whether you can suggest me some R packages >> designed for analyzing time course microarray data. > > > Yes, there appear to be several. > > Go to the bioconductor packages page: > > http://www.bioconductor.org/packages/release/bioc/ > > And search in that page for the word "time". I see at least three > packages there: > > * maSigPro > * Mfuzz > * timecourse > > There may be more ... I haven't used any of them, so I really can't > say too much more about it. > > HTH, > -steve > > -- > Steve Lianoglou > Graduate Student: Physiology, Biophysics and Systems Biology > Weill Medical College of Cornell University > > http://cbio.mskcc.org/~lianos > > _______________________________________________ > 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
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Hi Steve, Have a look at http://bioinfo.cipf.es/aconesa/research2.html and then the Asca-genes package (Nueda et al., 2007). Paper can be found at http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btm251v1 hope this helps! Johan --- On Thu, 2/12/09, Nishant Gopalakrishnan <ngopalak at="" fhcrc.org=""> wrote: > From: Nishant Gopalakrishnan <ngopalak at="" fhcrc.org=""> > Subject: Re: [BioC] Any package for time course microarray data analysis? > To: "Steve Lianoglou" <mailinglist.honeypot at="" gmail.com=""> > Cc: "BioC" <bioconductor at="" stat.math.ethz.ch=""> > Date: Thursday, February 12, 2009, 7:13 PM > Hi Steve > > You can make use of the Bioconductor task views to locate > specific > packages for analyzing time course micro array data. > > The bioconductor task views can be found at > > http://bioconductor.org/packages/release/BiocViews.html > > The views provided by biocViews integrate the software, > annotation data > and experiment data repositories provided by Bioconductor. > Basically the > biocViews field in the Description file of each package > determines the > views under which it appears in. > > For packages that deal with time course stuff please take a > look at the > TimeCourse subview under statistics. > > http://bioconductor.org/packages/release/TimeCourse.html > > Nishant > > > > Steve Lianoglou wrote: > > Hi, > > > >> Hi! I am wondering whether you can suggest me some > R packages > >> designed for analyzing time course microarray > data. > > > > > > Yes, there appear to be several. > > > > Go to the bioconductor packages page: > > > > http://www.bioconductor.org/packages/release/bioc/ > > > > And search in that page for the word "time". > I see at least three > > packages there: > > > > * maSigPro > > * Mfuzz > > * timecourse > > > > There may be more ... I haven't used any of them, > so I really can't > > say too much more about it. > > > > HTH, > > -steve > > > > -- > > Steve Lianoglou > > Graduate Student: Physiology, Biophysics and Systems > Biology > > Weill Medical College of Cornell University > > > > http://cbio.mskcc.org/~lianos > > > > _______________________________________________ > > 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 > > _______________________________________________ > 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
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