biosvd

DOI: 10.18129/B9.bioc.biosvd    

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

Package for high-throughput data processing, outlier detection, noise removal and dynamic modeling

Bioconductor version: 3.9

The biosvd package contains functions to reduce the input data set from the feature x assay space to the reduced diagonalized eigenfeature x eigenassay space, with the eigenfeatures and eigenassays unique orthonormal superpositions of the features and assays, respectively. Results of SVD applied to the data can subsequently be inspected based on generated graphs, such as a heatmap of the eigenfeature x assay matrix and a bar plot with the eigenexpression fractions of all eigenfeatures. These graphs aid in deciding which eigenfeatures and eigenassays to filter out (i.e., eigenfeatures representing steady state, noise, or experimental artifacts; or when applied to the variance in the data, eigenfeatures representing steady-scale variance). After possible removal of steady state expression, steady-scale variance, noise and experimental artifacts, and after re-applying SVD to the normalized data, a summary html report of the eigensystem is generated, containing among others polar plots of the assays and features, a table with the list of features sortable according to their coordinates, radius and phase in the polar plot, and a visualization of the data sorted according to the two selected eigenfeatures and eigenassays with colored feature/assay annotation information when provided. This gives a global picture of the dynamics of expression/intensity levels, in which individual features and assays are classified in groups of similar regulation and function or similar cellular state and biological phenotype.

Author: Anneleen Daemen <daemena at gene.com>, Matthew Brauer <matthejb at gene.com>

Maintainer: Anneleen Daemen <daemena at gene.com>, Matthew Brauer <matthejb at gene.com>

Installation

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

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

BiocManager::install("biosvd")

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("biosvd")

 

PDF	R Script	biosvd
PDF		Reference Manual
Text		NEWS

Details

biocViews	Software, TimeCourse, Visualization
Version	2.20.0
In Bioconductor since	BioC 2.14 (R-3.1) (5.5 years)
License	Artistic-2.0
Depends	R (>= 3.1.0)
Imports	BiocGenerics, Biobase, methods, grid, graphics, NMF
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Package Archives

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

Source Package	biosvd_2.20.0.tar.gz
Windows Binary	biosvd_2.20.0.zip
Mac OS X 10.11 (El Capitan)	biosvd_2.20.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/biosvd
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/biosvd
Package Short Url	https://bioconductor.org/packages/biosvd/
Package Downloads Report	Download Stats