下面是几个已知的单细胞marker基因数据库,点相应的加粗字体可以直达数据库官网: Mouse Cell Atlas CellMarker BD||cd_marker_handbook CancerSEA PanglaoDB haemosphere 造血过程关键基因表达谱数据库。 Haemosphere is a data portal designed for the bench biologist, providing intuitive interfaces to access and anal...
Single Cell Expression Atlas: https://www.ebi.ac.uk/gxa/sc/home SignatureDB: https://lymphochip.nih.gov/signaturedb/ KIT(肾脏单细胞数据库): http://humphreyslab.com/SingleCell/ 血管细胞数据库: http://betsholtzlab.org/VascularSingleCells/database.html 脑细胞数据库: https://web.stanford.e...
流程: 1. log : NormalizeData 2. 找特征 : FindVariableFeatures 3. 标准化 : ScaleData 4. pca : RunPCA 5. 构建图 : FindNeighbors 6. 聚类 : FindClusters 7. tsne /umap : RunTSNE RunUMAP 8. 差异基因 : FindAllMarkers / FindMarkers VlnPlot(raw_sce, features = c("percent.rp", "percen...
We curated a comprehensive cell marker database named scMayoMapDatabase and developed a companion R package scMayoMap, an easy-to-use single-cell annotation tool, to provide fast and accurate cell type annotation. The effectiveness of scMayoMap was demonstrated in 48 independent scRNA-seq dataset...
Cell type markers for each cell type were collected from previously published literature30,88,89,90,91 and the CellMarker database92. Cell type identity inference In general, lung cells were annotated based on the overall transcriptomic similarity with the reference data set and were combined with...
Saves the data in the DOM tree back to the part. This method can be called multiple times and each time it is called, the stream will be flushed. (Inherited from OpenXmlPartRootElement) Save(SingleCellTablePart) Saves the DOM into the SingleCellTablePart. Save(Stream) Saves ...
CellMarker: a manually curated resource of cell markers in human and mouse. Nucleic Acids Res. 47, D721–D728 (2019). Article CAS PubMed Google Scholar Cao, Y., Wang, X. & Peng, G. SCSA: a cell type annotation tool for single-cell RNA-seq data. Front. Genet. 11, 490 (2020)...
Bulk RNA数据基于细胞群体水平获得组织的平均特性,反映细胞群体的平均差异,而Single-cell RNA通过单个细胞的mRNA进行转录组分析,识别不同细胞亚群的细胞类型、状态和谱系,绘制细胞图谱、鉴定细胞异质性,可以精准解析细胞亚类功能及对疾病的影响[...
BiocManager::install("GSEABase") ##singleR(cell annotation)::must be locally installed ->make sure some dependency pakcages have been successfully installed-> ->search and download the target R package online("singleR" in this case)->
3a). We annotated cell types in this normal tissue using gene expression and gene activity scores of known marker genes (Extended Data Fig. 6a,b). A stem cell population with high expression and accessibility of LGR5, SMOC2, RGMB, PTPRO, EPHB2 and LRIG1 was evident (Extended Data Fig....