This package was removed from CRAN on 2018-06-01. Its history is shown below.

Reason: This package is now available from Bioconductor only, see <https://www.bioconductor.org/packages/release/bioc/html/mixOmics.html>

Details below reflect version 6.3.2, its last release before removal.

mixOmics

6.3.2

Omics Data Integration Project

18packages depend

–downloads / year

–test coverage

–checks pass

Overview

About

Maintained by Kim-Anh Le Cao29 releasesCRAN page ↗

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 variants of generalised Canonical Correlation Analysis, sparse Partial Least Squares and sparse Discriminant Analysis. Recently we implemented integrative methods to combine multiple data sets: N-integration with variants of Generalised Canonical Correlation Analysis and P-integration with variants of multi-group Partial Least Squares.

Install

BioconductorR (source archive)Ubuntu (r2u)

BiocManager::install("mixOmics")

Installs the current Bioconductor release. Requires the BiocManager package.

url <- "https://cran.r-project.org/src/contrib/Archive/mixOmics/mixOmics_6.3.2.tar.gz"
pkgFile <- "mixOmics_6.3.2.tar.gz"
download.file(url, pkgFile)
install.packages(pkgFile, type = "source", repos = NULL)

This package is no longer on CRAN, so install.packages() cannot fetch it by name. This downloads the last archived source (6.3.2) and builds it locally. Install its dependencies first, and note that building from source needs the usual compiler toolchain.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-mixomics

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled.

bspm (used by r2u) also needs make: sudo apt install make

Health

CRAN checks

CRAN check results are not tracked yet.

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

Dependencies · direct

Documentation

READMENoVignettesNopkgdown siteNoNEWSYes · 67% structuredCode of conductNoContributing guideNo

Examples that run: 94%
Documented parameters: 92%
Return-value docs: 85%
References docs: 74%

Downloads

Releases R versions

Daily download trend is not available in this view yet.

Compare downloads with other packages →

Also on904 r2u4.9K conda_forge2.7K bioconda67 c2d4u

Dependencies

Declared dependencies

12 external dependencies (excludes base and recommended)

Depends (4)

R >= 2.10MASSlatticeggplot2

Imports (13)

igraph rgl ellipse corpcor RColorBrewerparalleldplyr tidyr reshape2methodsmatrixStats rARPACK gridExtra

LinkingTo (0)

none

Suggests (0)

none

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

18direct

–indirect (not tracked)

mixKernel sgPLS Coxmos CytoProfile Holomics SISIR iTensor plsRcox plsmod xLLiM MSclassifR MetabolomicsBasics OmicNetR RVAideMemoire SelectBoost pctax recipes sharp

Code & Tests

People & History

People (9)

Other (9)

Kim-Anh Le Cao

Contributor

Florian Rohart

Contributor · added in 5.0-1

Ignacio Gonzalez

Contributor

Sebastien Dejean with key contributors Benoit Gautier

Contributor · added in 6.0.0

Francois Bartolo

Contributor · added in 6.0.0

contributions from Pierre Monget

Contributor · added in 5.0-4

Jeff Coquery

Contributor · added in 3.0

FangZou Yao

Contributor · added in 4.0-1

Show 1 more other

Benoit Liquet.

Contributor · added in 5.0-4

Listed in earlier versions (6)

Sebastien Dejean

no longer listed · 2.6 to 5.0-3

Pierre Monget

no longer listed · 2.8-1 to 3.0

Benoit Liquet

no longer listed · 4.0-1 to 5.0-3

Kim-Anh Le Cao with contributions from Pierre Monget

no longer listed · 4.0-1 to 5.0-3

Benoit Gautier

no longer listed · 5.0-4 to 5.2.0

Sebastien Dejean with key contributors Florian Rohart

no longer listed · 5.0-4 to 5.2.0

Package Timeline

29 releases. Pick two to compare their code metrics. R releases are shown for context.

R
R 3.6.0 released · 2019-04-26
6.3.2
2018-06-01 · diff ↗
6.3.2archived
2018-06-01 · diff ↗
This package is now available from Bioconductor only, see <https://www.bioconductor.org/packages/release/bioc/html/mixOmics.html>
R
R 3.5.0 released · 2018-04-23
6.3.1
2017-11-26 · diff ↗
6.3.0
2017-10-13 · diff ↗
6.2.0
2017-08-17 · diff ↗
6.1.3
2017-05-11 · diff ↗
R
R 3.4.0 released · 2017-04-21
6.1.2
2017-02-27 · diff ↗
6.1.1
2016-10-19 · diff ↗
6.1.0
2016-09-04 · diff ↗
6.0.0
2016-06-14 · diff ↗
R
R 3.3.0 released · 2016-05-03
5.2.0
2015-11-19 · diff ↗
5.1.2
2015-08-29 · diff ↗

Show 27 earlier events

5.1.1
2015-07-30 · diff ↗
5.0-4
2015-04-28 · diff ↗
R
R 3.2.0 released · 2015-04-16
R
R 3.1.0 released · 2014-04-10
R
R 3.0.0 released · 2013-04-03
5.0-3
2012-12-11 · diff ↗
5.0-2
2012-12-11 · diff ↗
5.0-1
2012-12-11 · diff ↗
4.1-5
2012-12-11 · diff ↗
4.1-4
2012-12-11 · diff ↗
4.1-3
2012-12-11 · diff ↗
R
R 2.15.0 released · 2012-03-30
R
R 2.14.0 released · 2011-10-31
4.0-2
2011-04-28 · diff ↗
4.0-1
2011-04-28 · diff ↗
3.0
2011-04-28 · diff ↗
2.9-6
2011-04-28 · diff ↗
R
R 2.13.0 released · 2011-04-13
R
R 2.12.0 released · 2010-10-15
R
R 2.11.0 released · 2010-04-22
2.9-4
2010-02-15 · diff ↗
2.9-2
2010-02-15 · diff ↗
2.9-1
2010-02-15 · diff ↗
2.8-1
2010-02-15 · diff ↗
2.7-1
2010-02-15 · diff ↗
2.6
2010-02-15
R
R 2.10.0 released · 2009-10-26

Package metadata

Total releases: 29
License: GPL (>= 2) OSI
Minimum R: ≥ 2.10
Bundled data: 2.9 MB / 14 files
Download size: not tracked yet
Installed size: not tracked yet
With dependencies: not tracked yet

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