兩款計算腫瘤純度的R包，
ESTIMATE： 利用表達數據計算基質與免疫評分，預測腫瘤純度；
ABSOLUTE ：是能夠定量腫瘤細胞純度、倍性、絕對拷貝數的包；
ESTIMATE就是一種預測腫瘤純度的工具，使用表達數據估計惡性腫瘤組織中的基質細胞和免疫細胞并且可以利用基因表達數據預測腫瘤組織中浸潤的基質/免疫細胞的存在。該算法基于單個樣本基因集合的富集分析，產生三個得分：
①基質評分（記錄腫瘤組織中基質的存在）
②免疫評分（代表腫瘤組織中免疫細胞的浸潤）
③估計分數（推斷腫瘤純度)
免疫微環境分析的兩種主流方法為CIBERSORT與ssGSEA
CIBERSORT：優勢：R包簡便，也有網頁在線操作優勢顯而易見。“LM22”文件中只有22種免疫細胞。?
ssGSEA ：根據輸入的gmt文件即可指定免疫細胞，之后對每個樣本計算出其免疫細胞的富集得分。其中最明顯的特征就是可以高度定制化。
[1]?Subramanian A, et al."Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles."Proc Natl Acad Sci U S A 2005, 102:15545-15550.
[2] Barbie DA, et al."Systematic RNA interference reveals that oncogenic KRAS-driven cancers require TBK1."Nature 2009, 462:108-112.
[3]?Verhaak RG, et al."Integrated genomic analysis identifies clinically relevant subtypes of glioblastoma characterized by abnormalities in PDGFRA, IDH1, EGFR, and NF1."Cancer Cell 2010, 17:98-110.
[1]?http://www.genepattern.org/modules/docs/ABSOLUTE/2
[2]?http://software.broadinstitute.org/cancer/cga/absolute_run
[3]?http://software.broadinstitute.org/cancer/software/genepattern/analyzing-absolute-data
[4]?Carter SL, Cibulskis K, Helman E, McKenna A, Shen H, Zack T, Laird PW, Onofrio RC, Winckler W, Weir BA, Beroukhim R, Pellman D, Levine DA, Lander ES, Meyerson M, Getz G. ?Absolute quantification of somatic DNA alterations in human cancer. Nat Biotechnol. 2012;30(5):413-21.
[1] GSVA: The Gene Set Variation Analysis package for microarray and RNA-seq data?
[2]?Xue Y, Tong L, LiuAnwei Liu F, et al. Tumor?infiltrating M2 macrophages driven by specific genomic alterations are associated with prognosis in bladder cancer. Oncol Rep. 2019;42(2):581-594.?doi:10.3892/or.2019.7196?
[3]?Jia Q, Wu W, Wang Y, et al. Local mutational diversity drives intratumoral immune heterogeneity in non-small cell lung cancer. Nat Commun. 2018;9(1):5361. Published 2018 Dec 18.?doi:10.1038/s41467-018-07767-w
