ETH Zurich, NEXUS Personalized Health Technologies, 8952 Schlieren, Switzerland.
SIB Swiss Institute of Bioinformatics, Zurich, Switzerland.
Bioinformatics. 2023 May 4;39(5). doi: 10.1093/bioinformatics/btad329.
Recently, CITE-seq emerged as a multimodal single-cell technology capturing gene expression and surface protein information from the same single cells, which allows unprecedented insights into disease mechanisms and heterogeneity, as well as immune cell profiling. Multiple single-cell profiling methods exist, but they are typically focused on either gene expression or antibody analysis, not their combination. Moreover, existing software suites are not easily scalable to a multitude of samples. To this end, we designed gExcite, a start-to-end workflow that provides both gene and antibody expression analysis, as well as hashing deconvolution. Embedded in the Snakemake workflow manager, gExcite facilitates reproducible and scalable analyses. We showcase the output of gExcite on a study of different dissociation protocols on PBMC samples.
gExcite is open source available on github at https://github.com/ETH-NEXUS/gExcite_pipeline. The software is distributed under the GNU General Public License 3 (GPL3).
最近，CITE-seq 作为一种多模式单细胞技术出现，能够从同一单细胞中捕获基因表达和表面蛋白信息，这使得人们能够以前所未有的方式深入了解疾病机制和异质性，以及免疫细胞分析。目前存在多种单细胞分析方法，但它们通常侧重于基因表达或抗体分析，而不是两者的结合。此外，现有的软件套件不容易扩展到大量样本。为此，我们设计了 gExcite，这是一个端到端的工作流程，提供基因和抗体表达分析，以及哈希去卷积。gExcite 嵌入在 Snakemake 工作流管理器中，便于可重复和可扩展的分析。我们在对 PBMC 样本的不同解离方案的研究中展示了 gExcite 的输出。
gExcite 是开源的，可在 github 上获得，网址为 https://github.com/ETH-NEXUS/gExcite_pipeline。该软件根据 GNU 通用公共许可证 3（GPL3）分发。
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