recipe bioconductor-kimod

A k-tables approach to integrate multiple Omics-Data

Homepage

https://bioconductor.org/packages/3.11/bioc/html/kimod.html

License

GPL (>=2)

Recipe

/bioconductor-kimod/meta.yaml

Links

biotools: kimod, doi: 10.1038/nmeth.3252

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.

package bioconductor-kimod

(downloads) docker_bioconductor-kimod

Versions

1.15.0-0, 1.14.0-0, 1.12.0-1, 1.10.0-0, 1.8.0-0, 1.6.0-0

Depends
Required By

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install bioconductor-kimod

and update with:

conda update bioconductor-kimod

or use the docker container:

docker pull quay.io/biocontainers/bioconductor-kimod:<tag>

(see bioconductor-kimod/tags for valid values for <tag>)