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Abstract |
Immune system is highly programmable in its cellular composition in response to external “foreign” stimuli. There is an intricate relationship between tumor cells and immune cells in the pathophysiological processes. Recent progress in single-cell RNA sequencing technology has allowed unprecedented dissection of the complex cancer immune microenvironment. Challenge remains as to the annotation and elucidation of the cell components and their interactions in the immune cellular ecosystems (ICEs). To this end, we developed immune cellular ecosystem explorer (ICExplorer) to facilitate in-depth annotation and visualization of immune cellular ecosystems (ICEs). ICExplorer includes a comprehensive cell marker list, a computational method, powered by a multi-objective optimization model, and a new visualization tool, Legoplot. ICExplorer advances the annotation of cell state transitions, elucidation of physically interacting cells regulating immune responses, and quantitative comparison of ICE changes. |
