mixOmics

Package: mixOmics
Type: Package
Title: Omics Data Integration Project
Version: 6.0.0
Date: 2016-06-13
Depends: R (>= 2.10), MASS, lattice, ggplot2
Imports: igraph, rgl, ellipse, corpcor, RColorBrewer, plyr, parallel,
dplyr, tidyr, reshape2, methods
Author: Kim-Anh Le Cao, Florian Rohart, Ignacio Gonzalez, Sebastien Dejean with key contributors Benoit Gautier, Francois Bartolo
and contributions from Pierre Monget, Jeff Coquery, FangZou Yao, Benoit Liquet.
Maintainer: Kim-Anh Le Cao <k.lecao@uq.edu.au>
Description: Multivariate methods are well suited to large omics data sets where the number of variables (e.g. genes, proteins, metabolites) is much larger than the number of samples (patients, cells, mice). They have the appealing properties of reducing the dimension of the data by using instrumental variables (components), which are defined as combinations of all variables. Those components are then used to produce useful graphical outputs that enable better understanding of the relationships and correlation structures between the different data sets that are integrated. mixOmics offers a wide range of multivariate methods for the exploration and integration of biological datasets with a particular focus on variable selection. The package proposes several sparse multivariate models we have developed to identify the key variables that are highly correlated, and/or explain the biological outcome of interest. The data that can be analysed with mixOmics may come from high throughput sequencing technologies, such as omics data (transcriptomics, metabolomics, proteomics, metagenomics etc) but also beyond the realm of omics (e.g. spectral imaging). The methods implemented in mixOmics can also handle missing values without having to delete entire rows with missing data. A non exhaustive list of methods include generalised Canonical Correlation Analysis, sparse Partial Least Squares and sparse Discriminant Analysis. Recently we implemented integrative methods to combine multiple data sets: horizontal integration with regularised Generalised Canonical Correlation Analysis and vertical integration with multi-group Partial Least Squares.
License: GPL (>= 2)
URL: http://www.mixOmics.org
BugReports: mixomics@math.univ-toulouse.fr or
https://bitbucket.org/klecao/package-mixomics/issues
Repository: CRAN
Date/Publication: 2016-06-14 12:08:22
Packaged: 2016-06-14 06:49:17 UTC; klecao
NeedsCompilation: no
LazyData: true

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'mixOmics' ...
** package 'mixOmics' successfully unpacked and MD5 sums checked
** R
** data
*** moving datasets to lazyload DB
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'mixOmics'
    finding HTML links ... done
    Koren.16S                               html  
    block.pls                               html  
    block.plsda                             html  
    block.spls                              html  
    block.splsda                            html  
    breast.TCGA                             html  
    breast.tumors                           html  
    cim                                     html  
    cimDiablo                               html  
    circosPlot                              html  
    colors                                  html  
    diverse.16S                             html  
    estim.regul                             html  
    explained_variance                      html  
    image.estim.regul                       html  
    image.tune.rcc                          html  
    imgCor                                  html  
    ipca                                    html  
    linnerud                                html  
    liver.toxicity                          html  
    logratio.transfo                        html  
    map                                     html  
    mat.rank                                html  
    mint.block.pls                          html  
    mint.block.plsda                        html  
    mint.block.spls                         html  
    mint.block.splsda                       html  
    mint.pls                                html  
    mint.plsda                              html  
    mint.spls                               html  
    mint.splsda                             html  
    mixOmics                                html  
    multidrug                               html  
    multilevel                              html  
    nearZeroVar                             html  
    network                                 html  
    nipals                                  html  
    nutrimouse                              html  
    pca                                     html  
    pcatune                                 html  
    perf                                    html  
    plot.perf                               html  
    plot.rcc                                html  
    plotArrow                               html  
    plotContrib                             html  
    plotDiablo                              html  
    plotIndiv                               html  
    plotLoadings                            html  
    plotVar                                 html  
    pls                                     html  
    plsda                                   html  
    predict                                 html  
    print.methods                           html  
    rcc                                     html  
    scatterutil                             html  
    selectVar                               html  
    sipca                                   html  
    spca                                    html  
    spls                                    html  
    splsda                                  html  
    srbct                                   html  
    stemcells                               html  
    study_split                             html  
    summary                                 html  
    tune                                    html  
    tune.mint.splsda                        html  
    tune.multilevel                         html  
    tune.pca                                html  
    tune.rcc                                html  
    tune.splsda                             html  
    unmap                                   html  
    vac18                                   html  
    vac18.simulated                         html  
    vip                                     html  
    withinVariation                         html  
    wrapper.rgcca                           html  
    wrapper.sgcca                           html  
    yeast                                   html  
** building package indices
** testing if installed package can be loaded
* DONE (mixOmics)
Making 'packages.html' ... done