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TiArA: A Virtual Appliance for the Analysis of Tiling Array Data
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 graphic...
Autores principales: | , , , , , |
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Formato: | Texto |
Lenguaje: | English |
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Public Library of Science
2010
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2848623/ https://www.ncbi.nlm.nih.gov/pubmed/20376318 http://dx.doi.org/10.1371/journal.pone.0009993 |
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author | Greenbaum, Jason A. Assarsson, Erika Chung, Jo L. Head, Steven Sette, Alessandro Peters, Bjoern |
author_facet | Greenbaum, Jason A. Assarsson, Erika Chung, Jo L. Head, Steven Sette, Alessandro Peters, Bjoern |
author_sort | Greenbaum, Jason A. |
collection | PubMed |
description | 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. |
format | Text |
id | pubmed-2848623 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2010 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-28486232010-04-07 TiArA: A Virtual Appliance for the Analysis of Tiling Array Data Greenbaum, Jason A. Assarsson, Erika Chung, Jo L. Head, Steven Sette, Alessandro Peters, Bjoern PLoS One Research Article 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. Public Library of Science 2010-04-01 /pmc/articles/PMC2848623/ /pubmed/20376318 http://dx.doi.org/10.1371/journal.pone.0009993 Text en Greenbaum et al. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited. |
spellingShingle | Research Article Greenbaum, Jason A. Assarsson, Erika Chung, Jo L. Head, Steven Sette, Alessandro Peters, Bjoern TiArA: A Virtual Appliance for the Analysis of Tiling Array Data |
title | TiArA: A Virtual Appliance for the Analysis of Tiling Array Data |
title_full | TiArA: A Virtual Appliance for the Analysis of Tiling Array Data |
title_fullStr | TiArA: A Virtual Appliance for the Analysis of Tiling Array Data |
title_full_unstemmed | TiArA: A Virtual Appliance for the Analysis of Tiling Array Data |
title_short | TiArA: A Virtual Appliance for the Analysis of Tiling Array Data |
title_sort | tiara: a virtual appliance for the analysis of tiling array data |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2848623/ https://www.ncbi.nlm.nih.gov/pubmed/20376318 http://dx.doi.org/10.1371/journal.pone.0009993 |
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