Recent advances in single-cell technologies have enabled the characterization of epigenomic heterogeneity at the cellular level. Computational methods for automatic cell type annotation are urgently needed given the exponential growth in the number of cells. In particular, annotation of single-cell chromati...
最后,如果有对一个sample中所有cell的cell type annotation信息,可以设想,Housekeeping gene由于它的普遍表达,应该是对cell type annotation不敏感的,因此我们可以利用cell type作为cluster label,对每一个gene基于ANOVA分析计算出一个F statistic量, N cells across P groups(cell types), withn_kcells in thekth gr...
使用我们开发的软件工具 GPTCelltype 查询 GPT-4(方法)。 对于竞争方法,我们评估了 GPT-3.5(GPT-4 的早期版本)以及 CellMarker2.0 、 SingleR和 ScType ,它们是自动细胞类型注释方法,提供适用于大量组织的参考(方法和补充表 1) )。 GPT-4 或竞争方法的细胞类型注释根据其与原始研究提供的手动注释的一致性进行...
Single-cell RNA-sequencing (scRNA-seq) has become a widely used tool for both basic and translational biomedical research. In scRNA-seq data analysis, cell type annotation is an essential but challenging step. In the past few years, several annotation tools have been developed. These methods req...
Here we demonstrate that the large language model GPT-4 can accurately annotate cell types using marker gene information in single-cell RNA sequencing analysis. When evaluated across hundreds of tissue and cell types, GPT-4 generates cell type annotation
基于以上需求,加拿大安大略省癌症研究所的研究人员设计了一个全面、泛癌的TME细胞类型分类工具scATOMIC(single cell annotation of tumour microenvironments in pan-cancer settings),通过反向层次分类和父节点重复消除的算法(RHC-REP)改进细胞分类,降低 TME 多细胞系统的转录组复杂性,对恶性和非恶性细胞进行模块化注释。
“Times” : The score of the first predicted celltype / The score of the second predicted celltype If you use SCSA for your research, please kindly cite the following paper: Cao Y, Wang X and Peng G (2020) SCSA: A Cell Type Annotation Tool for Single-Cell RNA-seq Data. Front. Gene...
Currently most methods take manual strategies to annotate cell types after clustering the single-cell RNA-seq data. Such methods are labor-intensive and heavily rely on user expertise, which may lead to inconsistent results. We present SCSA, an automatic tool to annotate cell types from single-ce...
For deconvolution and cell type annotation, single-cell RNA sequencing and ST data were integrated via the 'CARD' (v 1.1) [27] package with default settings. Initially, a 'CARD' object was created with the CreateCARDObject function, and the results were computed using CARD_deconvolution with ...
The development of single-cell and spatial transcriptomics methods was instrumental in the conception of the Human Cell Atlas initiative, which aims to generate an integrated map of all cells across the human body. These technology advances are bringing