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。
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...
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...
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
然后实现一些现成的模型来实现 embedding,以及 Cell type annotation。总共收集了233 data sets 和3.1 M cells,包含 45 个 organ。 具体方法如下 左侧是描述了提供的 data 和 model zoo 的部分,其中模型的 embedding 基本都是基于 Encoder-decoder 的,包括 NMF,AE,VAE等。细胞类型的预测是基于线性回归和MLP 的...
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...
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...
“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...
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 ...
scPML: pathway-based multi-view learning for cell type annotation from single-cell RNA-seq data Article Open access 14 December 2023 Fully-automated and ultra-fast cell-type identification using specific marker combinations from single-cell transcriptomic data Article Open access 10 March 2022 ...