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resources_for_r [2014/11/03 13:25]
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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 ===== Books on R ===== ===== Books on R =====
-   * **[[http://​www.amazon.com/​Numerical-Ecology-R-Use/​dp/​1441979751/​ref=sr_1_1?​ie=UTF8&​s=books&​qid=1294671360&​sr=8-1|Numerical Ecology with R]]** -  This new book by Borcard et al. from Université de Montréal discuss both some theory on quantitative methods in ecology and how they are implemented in the R language. ​ 
-   * **[[http://​www.icraf.com/​resources/​databases/​tree-diversity-analysis|Tree diversity analysis]]** - A free manual and software for common statistical methods for ecological and biodiversity studies. 
    * **[[http://​www.springer.com/​new+%26+forthcoming+titles+(default)?​SGWID=4-40356-404-173624787-6991|Use R - Book series]]** - These books are available online for free if your library is a subscriber. Titles include "​Forest Analytics with R", "​Functional Data Analysis with R and MATLAB",​ "A Primer of Ecology with R", "​Applied Spatial Data Analysis with R", etc.    * **[[http://​www.springer.com/​new+%26+forthcoming+titles+(default)?​SGWID=4-40356-404-173624787-6991|Use R - Book series]]** - These books are available online for free if your library is a subscriber. Titles include "​Forest Analytics with R", "​Functional Data Analysis with R and MATLAB",​ "A Primer of Ecology with R", "​Applied Spatial Data Analysis with R", etc.
    * **[[http://​www.cookbook-r.com/​|R cookbook - O'​reilly series]]** - This book contains over 200 "​recipes"​ (short practical examples). Great book to get started.    * **[[http://​www.cookbook-r.com/​|R cookbook - O'​reilly series]]** - This book contains over 200 "​recipes"​ (short practical examples). Great book to get started.
 +   * **[[http://​www.amazon.com/​Numerical-Ecology-R-Use/​dp/​1441979751/​ref=sr_1_1?​ie=UTF8&​s=books&​qid=1294671360&​sr=8-1|Numerical Ecology with R]]** -  This new book by Borcard et al. from Université de Montréal discuss both some theory on quantitative methods in ecology and how they are implemented in the R language. ​
 +   * **[[http://​www.icraf.com/​resources/​databases/​tree-diversity-analysis|Tree diversity analysis]]** - A free manual and software for common statistical methods for ecological and biodiversity studies.
    * **[[http://​emdbolker.wikidot.com/​|Ecological Models and Data in R]]** - This is a great book by Benjamin Bolker that covers multiple areas of ecological modeling, mostly in the bayesian framework. The associated wiki can be found [[http://​emdbolker.wikidot.com/​|here.]]    * **[[http://​emdbolker.wikidot.com/​|Ecological Models and Data in R]]** - This is a great book by Benjamin Bolker that covers multiple areas of ecological modeling, mostly in the bayesian framework. The associated wiki can be found [[http://​emdbolker.wikidot.com/​|here.]]
    * **[[http://​www.amazon.ca/​Extending-Linear-Model-Generalized-Nonparametric/​dp/​158488424X|Extending the Linear Model with R: Generalized Linear, Mixed Effects and Nonparametric Regression Models]]**    * **[[http://​www.amazon.ca/​Extending-Linear-Model-Generalized-Nonparametric/​dp/​158488424X|Extending the Linear Model with R: Generalized Linear, Mixed Effects and Nonparametric Regression Models]]**
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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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