1. coseq
  2. inst
  3. CITATION
Browse code

Clarify doc, update citations, add collapse_rows to plot function

Andrea M Rau authored on 08/06/2018 19:34:22
Showing 1 changed files
inst/CITATION
History View file @ cb2a986
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@@ -3,22 +3,24 @@ citHeader("To cite the R package 'coseq' in publications use:")
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 citEntry(entry   = "article",
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          title   = "Transformation and model choice for co-expression analysis of RNA-seq data",
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 		 journal = "Briefings in Bioinformatics",
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-         number  = "doi: http://dx.doi.org/10.1101/065607 ",
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-         year    = "2017",
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+         volume  = "19",
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+         number  = "3",
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+         pages   = "425-436",
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+         year    = "2018",
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          author  = personList(
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            person(given="Andrea", family="Rau"),
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 		   person(given="Cathy", family="Maugis-Rabusseau")),
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-         textVersion = "Rau, A. and Maugis-Rabusseau, C. (2017) Transformation and model choice for co-expression analayis of RNA-seq data. Briefings in Bioinformatics, doi: http://dx.doi.org/10.1101/065607.")
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+         textVersion = "Rau, A. and Maugis-Rabusseau, C. (2018) Transformation and model choice for co-expression analysis of RNA-seq data. Briefings in Bioinformatics, 19(3)-425-436.")
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 citEntry(entry   = "article",
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          title   = "Clustering transformed compositional data using K-means,
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            with applications in gene expression and bicycle sharing system data",
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-		 journal = "arXiv",
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-         number  = "arXiv:1704.06150",
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-         year    = "2017",
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+         journal = "Journal of Applied Statistics",
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+         number  = "doi:10.1080/02664763.2018.1454894",
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+         year    = "2018",
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          author  = personList(
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 		   person(given="Antoine", family="Godichon-Baggioni"),
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 		   person(given="Cathy", family="Maugis-Rabusseau"),
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            person(given="Andrea", family="Rau")),
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-         textVersion = "Godichon-Baggioni, A., Maugis-Rabusseau, C. and Rau, A. (2017) Clustering transformed compositional data using K-means,
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-         with applications in gene expression and bicycle sharing system data. arXiv:1704.06150.")
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+         textVersion = "Godichon-Baggioni, A., Maugis-Rabusseau, C. and Rau, A. (2018) Clustering transformed compositional data using K-means,
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+         with applications in gene expression and bicycle sharing system data. Journal of Applied Statistics, doi:10.1080/02664763.2018.1454894.")
Browse code

Add data and complete vignette

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/coseq@129071 bc3139a8-67e5-0310-9ffc-ced21a209358

Andrea Rau authored on 23/04/2017 22:29:32
Showing 1 changed files
inst/CITATION
History View file @ ffd8500
... ... 
@@ -4,8 +4,21 @@ citEntry(entry   = "article",
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          title   = "Transformation and model choice for co-expression analysis of RNA-seq data",
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 		 journal = "Briefings in Bioinformatics",
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          number  = "doi: http://dx.doi.org/10.1101/065607 ",
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-         year    = "2016",
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+         year    = "2017",
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          author  = personList(
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            person(given="Andrea", family="Rau"),
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 		   person(given="Cathy", family="Maugis-Rabusseau")),
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-         textVersion = "Rau, A. and Maugis-Rabusseau, C. (2016) Transformation and model choice for co-expression analayis of RNA-seq data. Briefings in Bioinformatics, doi: http://dx.doi.org/10.1101/065607.")
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+         textVersion = "Rau, A. and Maugis-Rabusseau, C. (2017) Transformation and model choice for co-expression analayis of RNA-seq data. Briefings in Bioinformatics, doi: http://dx.doi.org/10.1101/065607.")
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+
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+citEntry(entry   = "article",
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+         title   = "Clustering transformed compositional data using K-means,
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+           with applications in gene expression and bicycle sharing system data",
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+		 journal = "arXiv",
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+         number  = "arXiv:1704.06150",
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+         year    = "2017",
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+         author  = personList(
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+		   person(given="Antoine", family="Godichon-Baggioni"),
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+		   person(given="Cathy", family="Maugis-Rabusseau"),
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+           person(given="Andrea", family="Rau")),
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+         textVersion = "Godichon-Baggioni, A., Maugis-Rabusseau, C. and Rau, A. (2017) Clustering transformed compositional data using K-means,
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+         with applications in gene expression and bicycle sharing system data. arXiv:1704.06150.")
Browse code

Update kmeans plots and parallelization

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/coseq@128138 bc3139a8-67e5-0310-9ffc-ced21a209358

Andrea Rau authored on 06/04/2017 15:09:19
Showing 1 changed files
inst/CITATION
History View file @ 4deaebf
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@@ -8,4 +8,4 @@ citEntry(entry   = "article",
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          author  = personList(
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            person(given="Andrea", family="Rau"),
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 		   person(given="Cathy", family="Maugis-Rabusseau")),
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-         textVersion = "Rau, A. and Maugis-Rabusseau, C. (2016) Transformation and model choice for co-expression analayis of RNA-seq data. Briefings in Bioinformatics (to appear), doi: http://dx.doi.org/10.1101/065607.")
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+         textVersion = "Rau, A. and Maugis-Rabusseau, C. (2016) Transformation and model choice for co-expression analayis of RNA-seq data. Briefings in Bioinformatics, doi: http://dx.doi.org/10.1101/065607.")
Browse code

Adding TCseq, coseq

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/coseq@125426 bc3139a8-67e5-0310-9ffc-ced21a209358

Martin Morgan authored on 23/12/2016 20:17:03
Showing 1 changed files
inst/CITATION
History View file @ f544548
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new file mode 100644
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@@ -0,0 +1,11 @@
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+citHeader("To cite the R package 'coseq' in publications use:")
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+
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+citEntry(entry   = "article",
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+         title   = "Transformation and model choice for co-expression analysis of RNA-seq data",
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+		 journal = "Briefings in Bioinformatics",
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+         number  = "doi: http://dx.doi.org/10.1101/065607 ",
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+         year    = "2016",
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+         author  = personList(
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+           person(given="Andrea", family="Rau"),
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+		   person(given="Cathy", family="Maugis-Rabusseau")),
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+         textVersion = "Rau, A. and Maugis-Rabusseau, C. (2016) Transformation and model choice for co-expression analayis of RNA-seq data. Briefings in Bioinformatics (to appear), doi: http://dx.doi.org/10.1101/065607.")