consICA

This is the development version of consICA; for the stable release version, see consICA.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16

consensus Independent Component Analysis

Bioconductor version: Development (3.24)

consICA implements a data-driven deconvolution method – consensus independent component analysis (ICA) to decompose heterogeneous omics data and extract features suitable for patient diagnostics and prognostics. The method separates biologically relevant transcriptional signals from technical effects and provides information about the cellular composition and biological processes. The implementation of parallel computing in the package ensures efficient analysis of modern multicore systems.

Author: Petr V. Nazarov [aut, cre] ORCID: 0000-0003-3443-0298 , Tony Kaoma [aut] ORCID: 0000-0002-1269-4826 , Maryna Chepeleva [aut] ORCID: 0000-0003-3036-4916

Maintainer: Petr V. Nazarov <petr.nazarov at lih.lu>

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

Petr V. Nazarov, Tony Kaoma, Maryna Chepeleva. consICA: consensus Independent Component Analysis. doi:10.18129/B9.bioc.consICA, R package version 2.11.5, https://bioconductor.org/packages/consICA.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

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

## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")

BiocManager::install("consICA")

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("consICA")

The consICA package: User’s manual	HTML	R Script
Reference Manual	PDF
NEWS	Text
LICENSE	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Classification, FeatureExtraction, RNASeq, Sequencing, Software, StatisticalMethod, Technology, Transcriptomics
Version	2.11.5
In Bioconductor since	BioC 3.16 (R-4.2) (4 years)
License	MIT + file LICENSE
Depends	R (>= 4.2.0)
Imports	fastICA (>= 1.2.1), sm, org.Hs.eg.db, GO.db, stats, SummarizedExperiment, BiocParallel, graph, ggplot2, methods, Rfast, pheatmap, survival, topGO, graphics, grDevices
System Requirements
URL	https://github.com/biomod-lih/consICA
Bug Reports	https://github.com/biomod-lih/consICA/issues

Suggests	knitr, BiocStyle, rmarkdown, testthat, Seurat
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	consICA_2.11.5.tar.gz
Windows Binary (x86_64)	consICA_2.11.5.zip
macOS Binary (big-sur-x86_64)	consICA_2.11.5.tgz
macOS Binary (sonoma-arm64)	consICA_2.11.5.tgz
Source Repository	git clone https://git.bioconductor.org/packages/consICA
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/consICA
Package Short Url	https://bioconductor.org/packages/consICA/
Package Downloads Report	Download Stats