Preamble | Introduction | Setup | Retrieving the data-set | Create the COTAN object | Alternative ways to create a COTAN object | Assign to each cell its origin | Data cleaning | Plots from the raw counts | Dropping problematic cells | Check all good | Vignette clean-up stage

Preamble | Introduction | Setup | Retrieving the data-set | Create the COTAN object | Drop low quality cells | COTAN analysis | Differential Expression Analysis | Existing clusterizations | How to manipulate a clusterization | Clusters dendogram | Relevance of given marker genes | Find differentially expressed genes | Relevance of marker genes for the merge clusters | DEA cluster vs. cluster | Vignette clean-up stage

Preamble | Introduction | Setup | Retrieving the data-set | Create the COTAN object | Drop low quality cells | Establish Uniform Transcript cells' clusters | COTAN analysis | Uniform Clustering | First UT clusterization | Extract split clusters' statistics | Relevance of marker genes for the split clusters | UMAP of the split clusterization | Merged UT clusterization | Extract merge clusters' statistics | Relevance of marker genes for the merge clusters | UMAP of the merge clusterization | Vignette clean-up stage

Preamble | Introduction | Setup | Retrieving the data-set | Create the COTAN object | Drop low quality cells | Establish genes' clusters | COTAN analysis | Get data tables and stored COEX | Analysis of the elaborated data: GDI | Define genes lists | GDI Plot | Store the calibrated object for future analysis | Heatmaps | Establishing genes' clusters | UMAP plot | Vignette clean-up stage