Institute of Environmental Medicine, Karolinska Institutet, Solna 171 65, Sweden.
Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Solna 171 65, Sweden.
Mol Biol Evol. 2023 Dec 1;40(12). doi: 10.1093/molbev/msad267.
The burgeoning amount of single-cell data has been accompanied by revolutionary changes to computational methods to map, quantify, and analyze the outputs of these cutting-edge technologies. Many are still unable to reap the benefits of these advancements due to the lack of bioinformatics expertise. To address this issue, we present Ursa, an automated single-cell multiomics R package containing 6 automated single-cell omics and spatial transcriptomics workflows. Ursa allows scientists to carry out post-quantification single or multiomics analyses in genomics, transcriptomics, epigenetics, proteomics, and immunomics at the single-cell level. It serves as a 1-stop analytic solution by providing users with outcomes to quality control assessments, multidimensional analyses such as dimension reduction and clustering, and extended analyses such as pseudotime trajectory and gene-set enrichment analyses. Ursa aims bridge the gap between those with bioinformatics expertise and those without by providing an easy-to-use bioinformatics package for scientists in hoping to accelerate their research potential. Ursa is freely available at https://github.com/singlecellomics/ursa.
单细胞数据的大量涌现伴随着计算方法的革命性变化,这些方法用于绘制、量化和分析这些前沿技术的输出。由于缺乏生物信息学专业知识,许多人仍然无法从这些进展中受益。为了解决这个问题,我们提出了 Ursa,这是一个自动化的单细胞多组学 R 包,包含 6 个自动化的单细胞组学和空间转录组学工作流程。Ursa 允许科学家在基因组学、转录组学、表观基因组学、蛋白质组学和免疫组学领域在单细胞水平上进行定量后的单细胞或多组学分析。它通过为用户提供质量控制评估、多维分析(如降维和聚类)以及扩展分析(如伪时间轨迹和基因集富集分析)的结果,为用户提供了一站式分析解决方案。Ursa 的目标是通过为有生物信息学专业知识的人和没有生物信息学专业知识的人提供一个易于使用的生物信息学包,来弥合这一差距,希望能加速他们的研究潜力。Ursa 可在 https://github.com/singlecellomics/ursa 上免费获取。
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