mixOmics: Omics Data Integration Project

We provide statistical integrative techniques and variants to analyse highly dimensional data sets: regularized Canonical Correlation Analysis ('rCCA') and sparse Partial Least Squares variants ('sPLS') to unravel relationships between two heterogeneous data sets of size (n times p) and (n times q) where the p and q variables are measured on the same samples or individuals n. These data may come from high throughput technologies, such as 'omics' data (e.g. transcriptomics, metabolomics or proteomics data) that require an integrative or joint analysis. However, 'mixOmics' can also be applied to any other large data sets where p + q >> n. 'rCCA' is a regularized version of Canonical Correlation Analysis to deal with the large number of variables. 'sPLS' allows variable selection in a one step procedure and two frameworks are proposed: regression and canonical analysis. Numerous graphical outputs are provided to help interpreting the results. Recent methodological developments include: sparse PLS-Discriminant Analysis ('sPLS-DA'), Independent Principal Component Analysis ('IPCA'), multilevel analysis using variance decomposition of the data and integration of multiple data sets with regularized Generalised Canonical Correlation Analysis ('rGCCA') and variants (sparse 'GCCA'). More details can be found on our website.

Version: 5.0-4
Depends: R (≥ 2.10), MASS, lattice
Imports: RGCCA, igraph, rgl, pheatmap
Published: 2015-04-29
Author: Kim-Anh Le Cao, Ignacio Gonzalez, Sebastien Dejean with key contributors Florian Rohart, Benoit Gautier and contributions from Pierre Monget, Jeff Coquery, FangZou Yao, Benoit Liquet.
Maintainer: Kim-Anh Le Cao <k.lecao at uq.edu.au>
BugReports: mixomics@math.univ-toulouse.fr or https://bitbucket.org/klecao/package-mixomics/issues
License: GPL-2 | GPL-3 [expanded from: GPL (≥ 2)]
URL: http://www.mixOmics.org
NeedsCompilation: no
Materials: README NEWS
CRAN checks: mixOmics results

Downloads:

Reference manual: mixOmics.pdf
Package source: mixOmics_5.0-4.tar.gz
Windows binaries: r-devel: mixOmics_5.0-4.zip, r-release: mixOmics_5.0-4.zip, r-oldrel: mixOmics_5.0-4.zip
OS X Snow Leopard binaries: r-release: mixOmics_5.0-4.tgz, r-oldrel: mixOmics_5.0-4.tgz
OS X Mavericks binaries: r-release: mixOmics_5.0-4.tgz
Old sources: mixOmics archive

Reverse dependencies:

Reverse depends: bootsPLS, R2GUESS, sgPLS, YuGene
Reverse imports: plsRcox, RVAideMemoire
Reverse suggests: PLSbiplot1