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MineICA

Analysis of an ICA decomposition obtained on genomics data


Bioconductor version: Release (3.19)

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 "4.4") and enter:


if (!require("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")
MineICA: Independent component analysis of genomic data PDF R Script
Reference Manual PDF

Details

biocViews MultipleComparison, Software, Visualization
Version 1.44.0
In Bioconductor since BioC 2.12 (R-3.0) (11 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
System Requirements
URL
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Suggests biomaRt, GOstats, cluster, hgu133a.db, mclust, igraph, breastCancerMAINZ, breastCancerTRANSBIG, breastCancerUPP, breastCancerVDX, future, future.apply
Linking To
Enhances doMC
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Package Archives

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

Source Package MineICA_1.44.0.tar.gz
Windows Binary MineICA_1.44.0.zip
macOS Binary (x86_64) MineICA_1.44.0.tgz
macOS Binary (arm64) MineICA_1.44.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/MineICA
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/MineICA
Bioc Package Browser https://code.bioconductor.org/browse/MineICA/
Package Short Url https://bioconductor.org/packages/MineICA/
Package Downloads Report Download Stats