MineICA

DOI: 10.18129/B9.bioc.MineICA    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see MineICA.

Analysis of an ICA decomposition obtained on genomics data

Bioconductor version: 3.9

The goal of MineICA is to perform Independent Component Analysis (ICA) on multiple transcriptome datasets, integrating additional data (e.g molecular, clinical and pathological). This Integrative ICA helps the biological interpretation of the components by studying their association with variables (e.g sample annotations) and gene sets, and enables the comparison of components from different datasets using correlation-based graph.

Author: Anne Biton

Maintainer: Anne Biton <anne.biton at gmail.com>

Installation

To install this package, start R (version "3.6") and enter:

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

BiocManager::install("MineICA")

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("MineICA")

 

PDF	R Script	MineICA: Independent component analysis of genomic data
PDF		Reference Manual

Details

biocViews	MultipleComparison, Software, Visualization
Version	1.24.0
In Bioconductor since	BioC 2.12 (R-3.0) (6.5 years)
License	GPL-2
Depends	R (>= 2.10), methods, BiocGenerics(>= 0.13.8), Biobase, plyr, ggplot2, scales, foreach, xtable, biomaRt, gtools, GOstats, cluster, marray, mclust, RColorBrewer, colorspace, igraph, Rgraphviz, graph, annotate, Hmisc, fastICA, JADE
Imports	AnnotationDbi, lumi, fpc, lumiHumanAll.db
LinkingTo
Suggests	biomaRt, GOstats, cluster, hgu133a.db, mclust, igraph, breastCancerMAINZ, breastCancerTRANSBIG, breastCancerUPP, breastCancerVDX
SystemRequirements
Enhances	doMC
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	MineICA_1.24.0.tar.gz
Windows Binary	MineICA_1.24.0.zip
Mac OS X 10.11 (El Capitan)	MineICA_1.24.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/MineICA
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/MineICA
Package Short Url	https://bioconductor.org/packages/MineICA/
Package Downloads Report	Download Stats