kimod

DOI: 10.18129/B9.bioc.kimod    

This package is for version 3.11 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see kimod.

A k-tables approach to integrate multiple Omics-Data

Bioconductor version: 3.11

This package allows to work with mixed omics data (transcriptomics, proteomics, microarray-chips, rna-seq data), introducing the following improvements: distance options (for numeric and/or categorical variables) for each of the tables, bootstrap resampling techniques on the residuals matrices for all methods, that enable perform confidence ellipses for the projection of individuals, variables and biplot methodology to project variables (gene expression) on the compromise. Since the main purpose of the package is to use these techniques to omic data analysis, it includes an example data from four different microarray platforms (i.e.,Agilent, Affymetrix HGU 95, Affymetrix HGU 133 and Affymetrix HGU 133plus 2.0) on the NCI-60 cell lines.NCI60_4arrays is a list containing the NCI-60 microarray data with only few hundreds of genes randomly selected in each platform to keep the size of the package small. The data are the same that the package omicade4 used to implement the co-inertia analysis. The references in packages follow the style of the APA-6th norm.

Author: Maria Laura Zingaretti, Johanna Altair Demey-Zambrano, Jose Luis Vicente-Villardon, Jhonny Rafael Demey

Maintainer: M L Zingaretti <m.lau.zingaretti at gmail.com>

Installation

To install this package, start R (version "4.0") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("kimod")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("kimod")

 

PDF	R Script	kimod A K-tables approach to integrate multiple Omics-Data in R
PDF		Reference Manual
Text		NEWS

Details

biocViews	ExperimentData, GeneExpression, Microarray, Proteomics, Software, Visualization
Version	1.15.0
In Bioconductor since	BioC 3.3 (R-3.3) (4.5 years)
License	GPL (>=2)
Depends	R (>= 3.3), methods
Imports	cluster, graphics, Biobase
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	kimod_1.15.0.tar.gz
Windows Binary	kimod_1.15.0.zip
macOS 10.13 (High Sierra)
Source Repository	git clone https://git.bioconductor.org/packages/kimod
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/kimod
Package Short Url	https://bioconductor.org/packages/kimod/
Package Downloads Report	Download Stats