R Observatory: Metrics for mixOmics version 6.3.2

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

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

6.3.2Package record

Omics Data Integration Project

10packages dependsuggested by 11

–downloads / year

–test coverage

–flavors OK

Overview

About

Maintained by Kim-Anh Le CaoCRAN page ↗Website ↗

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)

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.

Health

CRAN checks

CRAN check results are not tracked yet.

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 6.3.2

READMEYes · 355 wordsVignettesNoNEWSYes · 67% structuredCitation fileYes · cites a publicationWebsiteYes

Help pages: 82
Examples that run: 77%49 run in a plain check · 9 never run · 6 hold no code
Exported functions with examples: 97%
Documented parameters: 92%
Return-value docs: 85%
Help pages citing references: 74%

How these are measured

Downloads

Releases R versions

Daily download trend is not available in this view yet.

Compare downloads with other packages →

Also on1.3K r2u5.3K conda_forge3.8K bioconda136 c2d4u

How downloads are counted

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

10direct

–indirect (not tracked)

Depends 2 · Imports 8

Suggested by 11

Show all 21 packagesHide all 21 packages

Depends, Imports or LinkingTo, most downloaded first

xLLiM plsRcox Coxmos plsmod mixKernel iTensor Holomics CytoProfile SISIR sgPLS

Suggests, most downloaded first

recipes RVAideMemoire tidypredict SelectBoost orbital MSclassifR sharp pctax MetabolomicsBasics OmicNetR specProc

How these are counted

Code & Tests

Datasets

People & History

People (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 personHide 1 person

Benoit Liquet.

Contributor · added in 5.0-4

Maintainer since 2.6 (2010)

Listed in earlier versions (5)

Show 5 peopleHide 5 people

Sebastien Dejean

no longer listed · 2.6 to 5.0-3

Pierre Monget

no longer listed · 2.8-1 to 5.0-3

Benoit Liquet

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

Releases (29)

Pick two releases to compare their code metrics.

R
R 3.6.0 released · 2019-04-26
6.3.2
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2018-06-01 · diff ↗ ·
added 1 export
tune.spls
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
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2017-11-26 · diff ↗ ·
removed 1 export
plotContrib
6.3.0
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2017-10-13 · diff ↗ ·
removed 1 export
tune.multilevel
6.2.0
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2017-08-17 · diff ↗
6.1.3
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2017-05-11 · diff ↗ ·
added 3 exports
background.predict, get.BER, get.confusion_matrix
R
R 3.4.0 released · 2017-04-21
6.1.2
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2017-02-27 · diff ↗ ·
removed 3 exports
scatterutil.base, scatterutil.eti, scatterutil.grid
6.1.1
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2016-10-19 · diff ↗ ·
added 1 export
mint.pca
6.1.0
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2016-09-04 · diff ↗ ·
removed 1 export
multilevel

added 2 exports
auroc, tune.block.splsda
6.0.0
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2016-06-14 · diff ↗ ·
removed 20 exports
bin.color, cov2, deflation, defl.select, ica.par, ica.def, initsvd, loo, l2.norm, Mfold, miscrossprod, pcasvd, scale2, s.match, soft_thresholding_L1, soft.threshold, sparsity, tau.estimate, tune.splsdalevel1, tune.splsdalevel2

added 23 exports
block.pls, block.plsda, block.spls, block.splsda, cimDiablo, circosPlot, explained_variance, logratio.transfo, mint.block.pls, mint.block.plsda, mint.block.spls, mint.block.splsda, mint.pls, mint.plsda, mint.spls, mint.splsda, mixOmics, plotDiablo, plotLoadings, study_split, tune, tune.mint.splsda, tune.splsda
R
R 3.3.0 released · 2016-05-03
5.2.0
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2015-11-19 · diff ↗ ·
removed 3 exports
pheatmap.multilevel, plot3dIndiv, plot3dVar

added 1 export
plotArrow
5.1.2
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2015-08-29 · diff ↗

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5.1.1
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2015-07-30 · diff ↗ ·
removed 2 exports
tau.estim, valid

added 13 exports
cov2, deflation, defl.select, initsvd, l2.norm, miscrossprod, plotContrib, scale2, soft_thresholding_L1, soft.threshold, sparsity, tau.estimate, wrapper.sgccda
5.0-4
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2015-04-28 · diff ↗ ·
removed 7 exports
check.one.level, jet.colors, multilevel.splsda, multilevel.spls, select.var, Split.variation.one.level, Split.variation.two.level

added 7 exports
color.jet, color.GreenRed, color.spectral, color.mixo, selectVar, tau.estim, withinVariation
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
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2012-12-11 · diff ↗ ·
added 1 export
valid
5.0-2
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2012-12-11 · diff ↗ ·
removed 3 exports
spls.model, splsda.model, valid

added 2 exports
check.one.level, perf
5.0-1
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2012-12-11 · diff ↗ ·
removed 5 exports
estim.regul, image.estim.regul, pcatune, q2.spls, q2.pls

added 5 exports
image.tune.rcc, tune.pca, tune.rcc, wrapper.rgcca, wrapper.sgcca
4.1-5
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2012-12-11 · diff ↗
4.1-4
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2012-12-11 · diff ↗
4.1-3
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2012-12-11 · diff ↗ ·
added 3 exports
select.var, spls.model, splsda.model
R
R 2.15.0 released · 2012-03-30
R
R 2.14.0 released · 2011-10-31
4.0-2
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2011-04-28 · diff ↗
4.0-1
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2011-04-28 · diff ↗ ·
added 10 exports
multilevel, multilevel.splsda, multilevel.spls, pheatmap.multilevel, Split.variation.one.level, Split.variation.two.level, tune.multilevel, tune.splsdalevel1, tune.splsdalevel2, tune.splslevel
3.0
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2011-04-28 · diff ↗ ·
added 4 exports
ica.par, ica.def, ipca, sipca
2.9-6
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2011-04-28 · diff ↗ ·
added 3 exports
nearZeroVar, q2.spls, q2.pls
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
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2010-02-15 · diff ↗ ·
added 3 exports
pcatune, pcasvd, spca
2.9-2
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2010-02-15 · diff ↗
2.9-1
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2010-02-15 · diff ↗
2.8-1
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2010-02-15 · diff ↗ ·
added 2 exports
map, unmap
2.7-1
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2010-02-15 · diff ↗ ·
added 4 exports
bin.color, pca, plsda, splsda
2.6
record
2010-02-15
R
R 2.10.0 released · 2009-10-26

Package metadata

First published: 2010-02-15
Total releases: 29 / 16 yrs
License: GPL (>= 2) OSI
Minimum R: ≥ 2.10
Bundled data: 2.9 MB / 14 files

Cite

Cite this package

Run in R for the authors' entry:

citation("mixOmics")

The package provides a citation file, so citation() returns the authors' own entry.

Cite the R Observatory

For a number measured here: a download total, a coverage figure, an archival date.

Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for mixOmics version 6.3.2 [Data set]. HJJB, LLC. Data release v2026-10-23. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-23, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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