MADE4: an R package for multivariate analysis of gene expression data

By A. Culhane, Jean Thioulouse, G. Perrière, Desmond G. Higgins. Bioinform., 2005

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Chemotherapy-resistant human AML stem cells home to and engraft within the bone-marrow endosteal region (2007, methodology): “Correspondence analysis using the same mRNA profiles was also performe”
Age-related changes in gut microbiota composition from newborn to centenarian: a cross-sectional study (2016, methodology): “CAGs were defined by a heat plot showing Kendall correlations between genera clustered by Pearson’s correlation coefficient and Ward’s linkage hierarchical clustering in R using the Made4 package [55] as previously described [42].”
A deep proteome and transcriptome abundance atlas of 29 healthy human tissues (2018, methodology): “Visualizing the transcriptome and proteome profiles in a plane using co-inertia analysis (CIA) (Culhane et al. 2005) indicate that mRNA and protein levels are more similar to each other within tissues than between tissues (Fig 3B) also reflected by an RV coefficient of 0.”
Gut microbiome of the Hadza hunter-gatherers (2014, methodology): “PCoA, and heatmap and bar plots were built using the packages Made4 (Culhane et al., 2005) and Vegan (http://cran.”