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>
citation("kimod")):
Installation
To install this package, start R (version "4.0") and enter:
if (!require("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")| kimod A K-tables approach to integrate multiple Omics-Data in R | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | ExperimentData, GeneExpression, Microarray, Proteomics, Software, Visualization |
| Version | 1.15.0 |
| In Bioconductor since | BioC 3.3 (R-3.3) (8 years) |
| License | GPL (>=2) |
| Depends | R (>= 3.3), methods |
| Imports | cluster, graphics, Biobase |
| System Requirements | |
| URL |
See More
| Suggests | |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
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| Links To Me | |
| Build Report | Build Report |
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 |
| Bioc Package Browser | https://code.bioconductor.org/browse/kimod/ |
| Package Short Url | https://bioconductor.org/packages/kimod/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.11 | Source Archive |