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Preprint

Diversity based on T cell composition

LZ Liangtao Zheng
SQ Shishang Qin
XH Xueda Hu
ZZ Zemin Zhang

Last updated date: Aug 15, 2022 Views: 578 Forks: 0

original An abbreviated version of this protocol was published in Science in Dec, 2021
Pan-cancer single-cell landscape of tumor-infiltrating T cells
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To compare the T cell composition among blood, normal tissues, and tumors, the frequency of CD4+ meta-clusters and CD8+ meta-clusters were calculated separately. Then a Shannon equitability index (normalized Shannon diversity index) (19) EH was calculated as:

 

Where pi  was the frequency of meta-cluster i, and M was the number of meta-clusters. The Shannon equitability index ranged from 0 to 1. While the high index indicated similar frequencies across different meta-clusters, the low index indicated certain meta-clusters dominated in the meta-cluster frequency distribution.

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How to cite：
Readers should cite both the Bio-protocol preprint and the original research article where this protocol was used:
  1. Zheng, L, Qin, S, Hu, X and Zhang, Z(2022). Diversity based on T cell composition. Bio-protocol Preprint. bio-protocol.org/prep1863.
  2. Zheng, L., Qin, S., Si, W., Wang, A., Xing, B., Gao, R., Ren, X., Wang, L., Wu, X., Zhang, J., Wu, N., Zhang, N., Zheng, H., Ouyang, H., Chen, K., Bu, Z., Hu, X., Ji, J. and Zhang, Z.(2021). Pan-cancer single-cell landscape of tumor-infiltrating T cells. Science 374(6574). DOI: 10.1126/science.abe6474

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