TiArA: a virtual appliance for the analysis of Tiling Array data.
Ontology highlight
ABSTRACT: Background
Genomic tiling arrays have been described in the scientific literature since 2003, yet there is a shortage of user-friendly applications available for their analysis.Methodology/principal findings
Tiling Array Analyzer (TiArA) is a software program that provides a user-friendly graphical interface for the background subtraction, normalization, and summarization of data acquired through the Affymetrix tiling array platform. The background signal is empirically measured using a group of nonspecific probes with varying levels of GC content and normalization is performed to enforce a common dynamic range.Conclusions/significance
TiArA is implemented as a standalone program for Linux systems and is available as a cross-platform virtual machine that will run under most modern operating systems using virtualization software such as Sun VirtualBox or VMware. The software is available as a Debian package or a virtual appliance at http://purl.org/NET/tiara.
SUBMITTER: Greenbaum JA
PROVIDER: S-EPMC2848623 | biostudies-literature | 2010 Apr
REPOSITORIES: biostudies-literature
Publications
TiArA: a virtual appliance for the analysis of Tiling Array data.
Greenbaum Jason A JA Assarsson Erika E Chung Jo L JL Head Steven S Sette Alessandro A Peters Bjoern B
PloS one 20100401 4
<h4>Background</h4>Genomic tiling arrays have been described in the scientific literature since 2003, yet there is a shortage of user-friendly applications available for their analysis.<h4>Methodology/principal findings</h4>Tiling Array Analyzer (TiArA) is a software program that provides a user-friendly graphical interface for the background subtraction, normalization, and summarization of data acquired through the Affymetrix tiling array platform. The background signal is empirically measured ...[more]
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