The singleCellBase provides a user-friendly interface to the scientific community to browse, search, download and submit records of marker genes and cell types. The resource providing ineluctable prior knowledge required by manual cell annotation, which is valuable to interpret scRNA-seq data and ...
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...
4.marker gene 数据库 众所周知,单细胞数据的分群结果是建立在数学逻辑上的,缺乏生物学意义。在鉴定每个群的细胞类型时,我们依赖已有的细胞类型特异表达的marker基因。因此,准确的marker基因是确定细胞类型的关键。该网站提供了不同物种、不同组织的marker基因列表。这些marker基因经过了RNA原位杂交或GFP报告基因表达的验...
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[...
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...
Integrating single-cell datasets produced by multiple omics technologies is essential for defining cellular heterogeneity. Mosaic integration, in which different datasets share only some of the measured modalities, poses major challenges, particularly re
3. DE analysis for clusters 0 and 4 identified the KLRD1 marker for natural killer (NK) cells20. Analysis of spatial transcriptomics data (CODEX) In addition to sequencing assays, recent imaging assays can also provide information on the expression of genes or proteins at the single-cell level...
MarkerMap: nonlinear marker selection for single-cell studies CellTree: an R/bioconductor package to infer the hierarchical structure of cell populations from single-cell RNA-seq data FLOW-MAP: a graph-based, force-directed layout algorithm for trajectory mapping in single-cell time course datasets...
CellMarker database v2 was integrated, the number of marker evidence increased from 48257 to 91969. User can use this version with cmd '-d whole_v2.db' instead. Download and Installation git clone https://github.com/bioinfo-ibms-pumc/SCSA.git pip install pandas numpy scipy openpyxl ...