Differences
This shows you the differences between two versions of the page.
Both sides previous revision Previous revision Next revision | Previous revision | ||
resources_for_r [2014/11/03 08:59] sebastien.renaut [R Packages for Genetics and Sequence Analyses] |
resources_for_r [2014/11/04 11:09] (current) sebastien.renaut [R Packages for Genetics and Sequence Analyses] |
||
---|---|---|---|
Line 2: | Line 2: | ||
===== Books on R ===== | ===== Books on R ===== | ||
+ | * **[[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.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.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.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://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]]** | ||
* **[[http://www.springerlink.com/content/978-0-387-87458-6#section=15123&page=1|Mixed Effects Models and Extensions in Ecology with R]]** by Zuur et al. | * **[[http://www.springerlink.com/content/978-0-387-87458-6#section=15123&page=1|Mixed Effects Models and Extensions in Ecology with R]]** by Zuur et al. | ||
- | |||
===== Resources for R ===== | ===== Resources for R ===== | ||
* **[[http://www.r-project.org/|Official R project homepage]]** | * **[[http://www.r-project.org/|Official R project homepage]]** | ||
Line 60: | Line 60: | ||
* **[[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. | ||
+ | |||
+ | |||
+ | |||
+ | |||