BioArray Software Environment (BASE): a platform for comprehensive management and analysis of microarray data.

Saal LH, Troein C, Vallon-Christersson J, Gruvberger S, Borg A, Peterson C.

Genome Biol. 2002 Jul 15;3(8):SOFTWARE0003. Epub 2002 Jul 15.

PMID: 12186655 [PubMed - indexed for MEDLINE]

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GeneXplorer: an interactive web application for microarray data visualization and analysis.

Rees CA, Demeter J, Matese JC, Botstein D, Sherlock G.

BMC Bioinformatics. 2004 Oct 1;5:141.

PMID: 15458579 [PubMed - indexed for MEDLINE]

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An introduction to BioArray Software Environment.

Troein C, Vallon-Christersson J, Saal LH.

Methods Enzymol. 2006;411:99-119. Review.

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KMD: an open-source port of the ArrayExpress microarray database.

Mainguy JP, Macdonnell G, Bund S, Wild DL.

Appl Bioinformatics. 2004;3(4):257-60.

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ArrayQuest: a web resource for the analysis of DNA microarray data.

Argraves GL, Jani S, Barth JL, Argraves WS.

BMC Bioinformatics. 2005 Dec 1;6:287.

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MARS: microarray analysis, retrieval, and storage system.

Maurer M, Molidor R, Sturn A, Hartler J, Hackl H, Stocker G, Prokesch A, Scheideler M, Trajanoski Z.

BMC Bioinformatics. 2005 Apr 18;6:101.

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arrayCGHbase: an analysis platform for comparative genomic hybridization microarrays.

Menten B, Pattyn F, De Preter K, Robbrecht P, Michels E, Buysse K, Mortier G, De Paepe A, van Vooren S, Vermeesch J, Moreau Y, De Moor B, Vermeulen S, Speleman F, Vandesompele J.

BMC Bioinformatics. 2005 May 23;6:124.

PMID: 15910681 [PubMed - indexed for MEDLINE]

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Biosphere: the interoperation of web services in microarray cluster analysis.

Cheung KH, de Knikker R, Guo Y, Zhong G, Hager J, Yip KY, Kwan AK, Li P, Cheung DW.

Appl Bioinformatics. 2004;3(4):253-6.

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2HAPI: a microarray data analysis system.

Fink JL, Drewes S, Patel H, Welsh JB, Masys DR, Corbeil J, Gribskov M.

Bioinformatics. 2003 Jul 22;19(11):1443-5.

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DNMAD: web-based diagnosis and normalization for microarray data.

Vaquerizas JM, Dopazo J, Díaz-Uriarte R.

Bioinformatics. 2004 Dec 12;20(18):3656-8. Epub 2004 Jul 9.

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Open source software for the analysis of microarray data.

Dudoit S, Gentleman RC, Quackenbush J.

Biotechniques. 2003 Mar;Suppl:45-51. Review.

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SeeGH--a software tool for visualization of whole genome array comparative genomic hybridization data.

Chi B, DeLeeuw RJ, Coe BP, MacAulay C, Lam WL.

BMC Bioinformatics. 2004 Feb 9;5:13.

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FGDP: functional genomics data pipeline for automated, multiple microarray data analyses.

Grant JD, Somers LA, Zhang Y, Manion FJ, Bidaut G, Ochs MF.

Bioinformatics. 2004 Jan 22;20(2):282-3.

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An XML message broker framework for exchange and integration of microarray data.

Tjandra D, Wong S, Shen W, Pulliam B, Yu E, Esserman L.

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AVA: visual analysis of gene expression microarray data.

Zhou Y, Liu J.

Bioinformatics. 2003 Jan 22;19(2):293-4.

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Gene expression data preprocessing.

Herrero J, Díaz-Uriarte R, Dopazo J.

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MADGE: scalable distributed data management software for cDNA microarrays.

McIndoe RA, Lanzen A, Hurtz K.

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The LCB Data Warehouse.

Ameur A, Yankovski V, Enroth S, Spjuth O, Komorowski J.

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SBEAMS-Microarray: database software supporting genomic expression analyses for systems biology.

Marzolf B, Deutsch EW, Moss P, Campbell D, Johnson MH, Galitski T.

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GeneCruiser: a web service for the annotation of microarray data.

Liefeld T, Reich M, Gould J, Zhang P, Tamayo P, Mesirov JP.

Bioinformatics. 2005 Sep 15;21(18):3681-2. Epub 2005 Jul 19.

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