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Raw gene expression data were extracted from the Scanpy object as recommended in the “Using 10x data” section (inferCNV of the Trinity CTAT Project, https://github.com/broadinstitute/inferCNV). Normal reference cells were identified from annotated Leiden clusters as naïve T cells. Tumor cells were identified as malignant-like cells in Leiden clusters. The inferCNV analysis was performed following the tutorial (https://github.com/broadinstitute/inferCNV/wiki) with parameters including default settings.
Copyright and License information: ©2021 Li, Wang, Dong, Man, Sun, Qian, Zhu, Cao, Yu, Le, Fu, Wang, Jiang, Shen, Ma, Chen, Xu, Shi, Zhang, Qian and Zhai
This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
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