作者，Evil Genius
生活不易，且行且珍惜，指不定哪天就找不见这个人了，这个举报速度，看来被人搞是注定的。
不知道大家怎么看WBG和BLG的半决赛。
今天我们更新方法，单细胞空间数据分析谱系追踪。
知识积累
肿瘤的进展是由癌细胞与其周围微环境之间的动态相互作用驱动的。研究肿瘤的时空演化可以提供重要的见解，了解癌细胞内部的变化和微环境的外部变化如何协同驱动肿瘤进展的不同阶段。在这个过程中，当癌细胞积累遗传和表观遗传改变时，微环境通过诸如空间限制、信号分子、养分和氧气有效性、免疫渗透等因素施加选择压力。反过来，肿瘤生长重塑了周围的微环境，例如，通过重组细胞外基质和改变浸润间质细胞的组成和状态。
核心分析点：肿瘤的进化动力学及其在原生空间背景下的微环境组成。
整合肿瘤系统发育分析，研究肿瘤内癌细胞的谱系关系，结合空间信息，为理解肿瘤微环境与进展之间的相互作用提供了一个全面的框架。
空间组学方法进一步阐明了基因组改变的空间分布如何导致克隆生长、具有不同驱动突变的亚克隆的分散、与免疫系统的相互作用以及转移。
高分辨率空间转录组学 + 谱系追踪功能
计算工具使空间分解的癌细胞系统发育推理成为可能
空转分辨率在肿瘤微环境的原生环境中建立癌症细胞的谱系，能够探索同一肿瘤中越来越相关的亚克隆的空间定位。
空间转录组学揭示肺腺癌的生态系统
肿瘤亚克隆快速扩张有助于形成缺氧区，降低癌细胞可塑性
亚克隆扩增伴随着免疫抑制和纤维化的微环境重塑
空间分辨的谱系揭示了原发肿瘤中引发转移诱导位点的进化
转移性定植伴有胶原沉积和纤维化增加
为了实现这个分析，需要很多的准备工作
convert: Convert the FASTQs into an unmapped BAM, while parsing any barcode and/or UMI sequences into BAM tags.
filter_bam: Filter reads with low-quality barcode and/or UMI sequences from the unmapped bam.
error_correct_cellbcs_to_whitelist**: For sequencing chemistries that have a predefined (cell) barcode whitelist, this steps perform correction of sequencing errors using this whitelist.
collapse: Collapse reads into UMIs by constructing one or more consensus sequences for each UMI using the set of reads with that UMI.
resolve: Resolve a single sequence for each UMI by choosing the most likely sequencing read to represent each UMI in a cell.
align: Align sequences to the reference target site using the Smith-Waterman local alignment algorithm.
call_alleles: Call alleles with respect to the reference target site and the alignment of a sequence, thereby reporting the set of mutations that a target site sequence contains.
error_correct_intbcs_to_whitelist: For experimental designs for which each target site vector molecule has a unique barcode (“intBC”), and the set of intBCs present in the sequenced sample are known beforehand, this step performs sequencing error correction of these intBCs to the provided whitelist.
error_correct_umis: Error-correct UMIs whose mutation data is identical and whose UMI barcode sequences are similar enough.
filter_molecule_table: Filter UMIs that have conflicting allele information, too few reads, or do not meet other quality control criteria.
call_lineages: Split up cells into clonal populations, based on their shared set of integration barcodes (intBCs).
