The creole package is a series of tools designed to estimate gene expression trends through pseudo- or development-time given single-cell RNA- seq data. The code is designed in three parts. creole_map models the data in a low-dimensional space and calculates lineage divergence and a putative origin. Creole_lines estimates a fine-resolution pseudo-temporal signal for each input gene through each lineage. Creole_plot shows this data visually and creates figures to facilitate an interpretation of the data presented.
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