:: DESCRIPTION
VarMixt is an efficient variance modelling for the differential analysis of replicated gene expression data.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2005 Feb 15;21(4):502-8.
VarMixt: efficient variance modelling for the differential analysis of replicated gene expression data.
Delmar P, Robin S, Daudin JJ.
:: DESCRIPTION
OsCAS (Oryza sativa Chips Annotation System) is a comprehensive system designed to annotate the results of rice microarray experiments and analysis relationships between genes based on their expression. The aim of the platform is to facilitate the study of differently expressed genes in the microarray experiments within the framework of systems biological research.
::DEVELOPER
Ming Chen’s Bioinformatics Group, Zhejiang University.
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Qingyun Shi, Yijun Meng, Dijun Chen, Fei He, Haibin Gu, Ping Wu, Ming Chen(2010)
OsCAS: a comprehensive web-based annotation platform for rice microarray data.
BioChip Journal, 4(1): 9-15.
:: DESCRIPTION
PageMan is a tool to get a quick overview of multiparallel experiments. PageMan also helps comparing experiments from different organisms.
::DEVELOPER
Max Planck Institute for Molecular Plant Physiology
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Usadel B, Nagel A, Steinhauser D, Gibon Y, Blaesing OE, Redestig H, Sreenivasulu N, Krall L, Hannah MA, Poree F, Fernie AR, Stitt M (2006)
PageMan an interactive ontology tool to generate, display, and annotate overview graphs for profiling experiments,
BMC Bioinformatics 18:7:535
:: DESCRIPTION
ArrayMining is a server for automating statistical analysis of gene and protein expression microarray data, designed as a supporting tool for investigation of the genetic components of diseases.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
BMC Bioinformatics. 2009 Oct 28;10:358. doi: 10.1186/1471-2105-10-358.
ArrayMining: a modular web-application for microarray analysis combining ensemble and consensus methods with cross-study normalization.
Glaab E, Garibaldi JM, Krasnogor N.
:: DESCRIPTION
ReMoDiscovery is an intuitive algorithm to correlate regulatory programs with regulators and corresponding motifs to a set of co-expressed genes. It exploits in a concurrent way three independent data sources: ChIP-chip data, motif information and gene expression profiles.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: MORE INFORMATION
Citation
Genome Biol. 2006;7(5):R37. Epub 2006 May 5.
Inferring transcriptional modules from ChIP-chip, motif and microarray data.
Lemmens K, Dhollander T, De Bie T, Monsieurs P, Engelen K, Smets B, Winderickx J, De Moor B, Marchal K.
:: DESCRIPTION
GoSurfer uses Gene Ontology (GO) information to analyze gene sets obtained from genome-wide computations or microarray analyses. GoSurfer is a graphical interactive data mining tool. It associates user input genes with GO terms and visualizes such GO terms as a hierarchical tree. Users can manipulate the tree output by various means, like setting heuristic thresholds or using statistical tests. Significantly important GO terms resulted from a statistical test can be highlighted. All related information are exportable either as texts or as graphics.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Zhong S, Storch F, Lipan O, Kao MJ, Weitz C, Wong WH.
GoSurfer: a graphical interactive tool for comparative analysis of large gene sets in Gene Ontology space.
Applied Bioinformatics 2004, 3(4): 1-5.
:: DESCRIPTION
RPS (Reproducibility Probability Score) computes reproducibility probability score to select differentially expressed genes. The Reproducibility Probability Score (RPS), takes into consideration both the replicated data in a particular lab and the measurement variability across labs. The measurement variability is assessed by utilizing the reference gene expression data generated in the Microarray Quality Control (MAQC) project. Specifically, we applied the data generated across replicate gene expression analysis that was conducted in multiple facilities as part of this effort. A larger RPS means a gene is more likely to be differentially expressed; and if similar transcription profiling measurements are made in other laboratories, it is highly likely to be confirmed.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Guixian Lin, Xuming He, Hanlee Ji, Leming Shi, Ronald W. Davis, and Sheng Zhong.
Reproducibility Probability Score: Incorporating Measurement Variability across Laboratories for Gene Selection,
Nature Biotechnology 24, 1476 – 1477 (2006)
:: DESCRIPTION
SKNN (SeqKnn) imputes the missing values sequentially from the gene having least missing values, and uses the imputed values for the later imputation
:: DEVELOPER
Bioinformatics and Synthetic Biology Lab, KAIST.
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
BMC Bioinformatics. 2004 Oct 26;5:160.
Reuse of imputed data in microarray analysis increases imputation efficiency.
Kim KY, Kim BJ, Yi GS.
:: DESCRIPTION
Genetrix is an next-generation software that brings the full power of proven statistical methods, powerful machine-learning heuristics and integrated biological knowledge to the analysis and interpretation of gene expression, RNA, μRNA, SNP and DNA methylation microarray experiments.
::DEVELOPER
:: SCREENSHOTS
::REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
DetectiV is a package for R containing functions for visualisation, normalisation and significance testing of pathogen detection microarray data. DetectiV uses simple and established methods for visualisation, normalisation and significance testing. When applied to a publicly available microarray dataset, DetectiV produces the correct result in 55 out of 56 arrays tested, an improvement on previously published methods.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
DetectiV: visualization, normalization and significance testing for pathogen-detection microarray data.
Watson M, Dukes J, Abu-Median AB, King DP, Britton P.
Genome Biol. 2007;8(9):R190.
