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Provides class infrastructure and associated methods to construct an Illumina analysis workflow pipeline starting with raw data through functional analysis. Besides supporting the existing algorithms for microarray data, the lumi package includes several unique parts: (i) a variance-stabilizing transformation that utilizes the technical replicates available on the Illumina microarray; (ii) normalization algorithms designed for Illumina microarray data and; iii) the nucleotide universal identifier annotation packages.

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lumi classification

lumi specifications

Software type:
Package
Restrictions to use:
None
Operating system:
Unix/Linux, Mac OS, Windows
License:
GNU Lesser General Public License version 3.0
Version:
2.26.4
Requirements:
R
Interface:
Command line interface
Biological technology:
Illumina
Programming languages:
R
Computer skills:
Advanced
Stability:
Stable

lumi support

Documentation

Credits

Publications

  • (Lin et al., 2008) Model-based variance-stabilizing transformation for Illumina microarray data. Nucleic Acids Research.
    Published on: 2008 Feb 01
    PMID: 18178591

Institution(s)

Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL, USA

Link to literature

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