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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] (current) 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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