Package: biosvd
Type: Package
Title: Package for high-throughput data processing, outlier detection,
        noise removal and dynamic modeling
Version: 2.4.0
Date: 2014-10-08
Author: Anneleen Daemen <daemena@gene.com>, Matthew Brauer
    <matthejb@gene.com>
Maintainer: Anneleen Daemen <daemena@gene.com>, Matthew Brauer
 <matthejb@gene.com>
Description: 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.
License: Artistic-2.0
Depends: R (>= 3.1.0)
Imports: BiocGenerics, Biobase, methods, grid, graphics, NMF
biocViews: TimeCourse, Visualization
Packaged: 2015-04-17 04:50:47 UTC; biocbuild
NeedsCompilation: no
Built: R 3.2.0; ; 2015-04-17 06:49:09 UTC; windows
