clusterExperiment and RSEC: A Bioconductor package and framework for clustering of single-cell and other large gene expression datasets
Fig 2
Biomarker detection, demonstrated on the olfactory epithelium dataset.
Heatmap from the plotHeatmap function showing genes found differentially expressed (DE) between clusters by the function getBestFeatures, using both the global F-statistic (a) and hierarchical contrasts (b) options. Each of the contrasts in (b) corresponds to nodes in the dendrogram color-coded as in Fig 1d; we retained only the top 50 DE genes per node. Genes found DE in multiple contrasts may be plotted multiple times. For comparison purposes, in (a), we retained the top 256 DE genes according to a global F-statistic, where 256 is the number of unique genes in the hierarchical contrasts shown in (b).