OSCA单细胞数据分析笔记11—Cell type annotation 分享是一种态度 对应原版教程第12章http://bioconductor.org/books/release/OSCA/overview.html “物以类聚”的类是什么类?比如将一群水果分为不同的类群,则又红又圆特征的可能是苹果。对于单细胞聚类的结果,类的最直接注释就是细胞类型。本节将学习单细胞数据分析...
In fact, annotating cell-types in scATAC-seq data is a challenging task since, unlike in scRNA-seq data, we lack knowledge of 'marker regions' which could be used for cell-type annotation. Current annotation methods typically translate accessibility to expression space and rely on g...
# Cell type annotation by GPT-4 res <- gptcelltype(markers, model = 'gpt-4') # Assign cell type annotation back to Seurat object obj@meta.data$celltype <- as.factor(res[as.character(Idents(obj))]) # Visualize cell type annotation on UMAP DimPlot(obj,group.by='celltype') 而且如果...
Consistent annotation transfer from reference dataset to query dataset is fundamental to the development and reproducibility of single-cell research. Compared with traditional annotation methods, deep learning based methods are faster and more automated.
相信这些问题已经困扰大家很久了,那么这篇题为"Assessing GPT-4 for cell type annotation in single-cell RNA-seq analysis"的文章能够一定程度上医好大家的头疼。 原文链接 :https://www.nature.com/articles/s41592-024-02235-4 二、主要内容 细胞注释是 single-cell RNA suquencing(scRNA-seq)的基本步骤,...
作者基于大语言模型开发了一个新的细胞注释工具mLLMCelltype,在单细胞 RNA 测序的细胞类型注释方面表现卓越,大幅提升了注释精度,相关研究成果《Large Language Model Consensus Substantially Improves the Cell Type Annotation Accuracy for scRNA-seq Data》已在预印本平台bioRxiv [1]上发表。 工作流程 首先,通过差异...
This example uses Census to predict cell-types in lung cell atlas data from Travaglini et al, Nature 2020. First the data needs to be processed using the standard Seurat pipeline to produce a UMAP dimensionality reduction. Next, run thecensus_mainfunction for cell-type annotation. ...
an automatic tool to annotate cell types from single-cell RNA-seq data, based on a score annotation model combining differentially expressed genes and confidence levels of cell markers in databases. Evaluation on real scRNA-seq datasets that SCSA is able to assign the cells into the correct types...
12Altmetric Metrics Abstract 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, annota...
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 to