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resources_for_r [2014/11/03 13:28]
sebastien.renaut [Books on R]
resources_for_r [2014/11/04 11:09]
sebastien.renaut [R Packages for Genetics and Sequence Analyses]
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   * **[[http://​cran.r-project.org/​web/​packages/​hierfstat/​index.html|hierfstat]]** - Exploratory analyses for the phylogenetic comparative method. - hierarchical F-statistics from genetic data (e.g. Fst value)   * **[[http://​cran.r-project.org/​web/​packages/​hierfstat/​index.html|hierfstat]]** - Exploratory analyses for the phylogenetic comparative method. - hierarchical F-statistics from genetic data (e.g. Fst value)
   * **[[http://​cran.r-project.org/​web/​packages/​ape/​index.html|ape]]** - Reading, writing, plotting, and manipulating phylogenetic trees. Analyses of comparative data in a phylogenetic framework in general.   * **[[http://​cran.r-project.org/​web/​packages/​ape/​index.html|ape]]** - Reading, writing, plotting, and manipulating phylogenetic trees. Analyses of comparative data in a phylogenetic framework in general.
 +  * **[[http://​www.bioconductor.org/​packages/​release/​bioc/​html/​edgeR.html|edgeR]]** - A Bioconductor package for differential expression analysis of digital gene expression data.
 +  * **[[http://​bioconductor.org/​packages/​release/​bioc/​html/​DESeq.html|DESeq]]** - Another Bioconductor package for differential expression analysis of digital gene expression data, based on the negative binomial distribution.
 +  * **[[http://​www.bioconductor.org/​packages/​release/​bioc/​html/​DEGseq.html|DEGseq]]** - Yet another Bioconductor package to identify differentially expressed genes from RNA-seq data.
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