Differences

This shows you the differences between two versions of the page.

--- resources_for_r [2011/03/04 21:02]
csbq_qcbs
+++ resources_for_r [2014/11/04 16:09] (current)
sebastien.renaut [R Packages for Genetics and Sequence Analyses]
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 ===== 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.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://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.
 ===== Resources for R =====
   * **[[http://www.r-project.org/|Official R project homepage]]**
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   * **[[http://cran.r-project.org/web/packages/cluster/index.html|cluster]]** - Cluster analysis extended.
   * **[[http://cran.r-project.org/web/packages/amap/index.html|amap]]** - Another Multidimensional Analysis Package, tools for Clustering and Principal Component Analysis.
-===== R Packages for Genetics and Molecular Biology =====
+===== R Packages for Genetics and Sequence Analyses =====
   * **[[http://cran.univ-lyon1.fr/web/packages/adegenet/index.html|adegenet]]** - Classes and methods for the multivariate analysis of genetic markers.
   * **[[http://cran.r-project.org/web/packages/adephylo/index.html|adephylo]]** - Exploratory analyses for the phylogenetic comparative method.
+  * **[[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://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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