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>

Citation (from within R, enter citation("MineICA")):

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

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: