9) TM4 Microarray Software Suite

By A. Saeed, N. Bhagabati, J. Braisted, W. Liang, V. Sharov, E. Howe, Jianwei Li, M. Thiagarajan, J. White, John Quackenbush. 2006

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TagFinder for the quantitative analysis of gas chromatography - mass spectrometry (GC-MS)-based metabolite profiling experiments (2008, methodology): “We recommend the TM4 multi-experiment viewer (Saeed et al., 2003; Saeed et al., 2006) for a first visual assessment.”
Human BAT Possesses Molecular Signatures That Resemble Beige/Brite Cells (2012, methodology): “The measured mRNA expression were clustered according to the gene group and visualized as a heatmap representation using Multi Experiment Viewer [31].”
High-fat diet alters gut microbiota physiology in mice (2013, methodology): “The filtered matrix was analyzed using Hierarchical Clustering Explorer (College Park, MD, USA) (Seo and Shneiderman, 2002) for unsupervised multivariate data analysis and MultiExperiment Viewer (Saeed et al., 2006) for calculation of significant masses by two-tailed Student’s t-test (adjusted P-val”
RNA-Seq analysis in MeV (2011, neutral): “Here, we report the adaptation of the MeV (Saeed et al., 2003, 2006) gene expression analysis tool for this purpose.”