Chipster: user-friendly analysis software for microarray and other high-throughput data

BMC Genomics

Software

Eija I Korpelainen¹  M Aleksi Kallio¹  Petri Klemelä¹  Massimiliano Gentile¹  Taavi Hupponen¹  Jarno T Tuimala²  Janne Käki³  Mikko Koski³  Ilari Scheinin⁴ 

[1] CSC - IT Center for Science, Keilaranta 14, Keilaniemi, Espoo, Finland;CSC - IT Center for Science, Keilaranta 14, Keilaniemi, Espoo, Finland;Finnish Red Cross Blood Service, Kivihaantie 7, Helsinki, Finland;CSC - IT Center for Science, Keilaranta 14, Keilaniemi, Espoo, Finland;Futurice, Vattuniemenranta 2, Helsinki, Finland;Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands;Department of Pathology, Haartman Institute and HUSLAB, University of Helsinki and Helsinki University Central Hospital, Finland;FIMM Technology Centre, Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Finland;

关键词: Gene Ontology;    Interactive Visualization;    Exon Array;    Analysis Session;    aCGH Data;   

DOI  :  10.1186/1471-2164-12-507

 received in 2011-07-01, accepted in 2011-10-14,  发布年份 2011

来源: Springer

【 摘 要 】

BackgroundThe growth of high-throughput technologies such as microarrays and next generation sequencing has been accompanied by active research in data analysis methodology, producing new analysis methods at a rapid pace. While most of the newly developed methods are freely available, their use requires substantial computational skills. In order to enable non-programming biologists to benefit from the method development in a timely manner, we have created the Chipster software.ResultsChipster (http://chipster.csc.fi/) brings a powerful collection of data analysis methods within the reach of bioscientists via its intuitive graphical user interface. Users can analyze and integrate different data types such as gene expression, miRNA and aCGH. The analysis functionality is complemented with rich interactive visualizations, allowing users to select datapoints and create new gene lists based on these selections. Importantly, users can save the performed analysis steps as reusable, automatic workflows, which can also be shared with other users. Being a versatile and easily extendable platform, Chipster can be used for microarray, proteomics and sequencing data. In this article we describe its comprehensive collection of analysis and visualization tools for microarray data using three case studies.ConclusionsChipster is a user-friendly analysis software for high-throughput data. Its intuitive graphical user interface enables biologists to access a powerful collection of data analysis and integration tools, and to visualize data interactively. Users can collaborate by sharing analysis sessions and workflows. Chipster is open source, and the server installation package is freely available.

【 授权许可】

Unknown   
© Kallio et al; licensee BioMed Central Ltd. 2011. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.