TIMEx：利用泛癌单细胞RNA测序特征对大量转录组学进行肿瘤免疫微环境反卷积的网络门户。
TIMEx: tumor-immune microenvironment deconvolution web-portal for bulk transcriptomics using pan-cancer scRNA-seq signatures.
作者信息
Xie Mengyu, Lee Kyubum, Lockhart John H, Cukras Scott D, Carvajal Rodrigo, Beg Amer A, Flores Elsa R, Teng Mingxiang, Chung Christine H, Tan Aik Choon
机构信息
Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA.
Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA.
出版信息
Bioinformatics. 2021 Oct 25;37(20):3681-3683. doi: 10.1093/bioinformatics/btab244.
Abstract
SUMMARY
The heterogeneous cell types of the tumor-immune microenvironment (TIME) play key roles in determining cancer progression, metastasis and response to treatment. We report the development of TIMEx, a novel TIME deconvolution method emphasizing on estimating infiltrating immune cells for bulk transcriptomics using pan-cancer single-cell RNA-seq signatures. We also implemented a comprehensive, user-friendly web-portal for users to evaluate TIMEx and other deconvolution methods with bulk transcriptomic profiles.
AVAILABILITY AND IMPLEMENTATION
TIMEx web-portal is freely accessible at http://timex.moffitt.org.
SUPPLEMENTARY INFORMATION
Supplementary data are available at Bioinformatics online.
摘要
摘要
肿瘤免疫微环境（TIME）中的异质细胞类型在决定癌症进展、转移及治疗反应方面发挥着关键作用。我们报告了TIMEx的开发，这是一种新型的TIME反卷积方法，重点是利用泛癌单细胞RNA测序特征估计批量转录组学中的浸润免疫细胞。我们还为用户实现了一个全面、用户友好的网络门户，以便用户使用批量转录组学概况评估TIMEx和其他反卷积方法。
可用性和实现方式
TIMEx网络门户可通过http://timex.moffitt.org免费访问。
补充信息
补充数据可在《生物信息学》在线获取。
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