3.Park J , Shrestha R , Qiu C , et al. Single-cell transcriptomics of the mouse kidney reveals potential cellular targets of kidney disease[J]. Science, 2018:eaar2131. 4.Zhang X, Lan Y, Xu J, et al. CellMarker: a manually curated resource of cell markers in human and mouse[J]....
et al. Comprehensive mapping of tissue cell architecture via integrated single cell and spatial transcriptomics. bioRxiv https://doi.org/10.1101/2020.11.15.378125 (2020). Article Google Scholar Zhang, X. et al. CellMarker: a manually curated resource of cell markers in human and mouse. Nucleic...
We used known cell markers for the well characterized immune cells (B cell, T cell, NK cell, and macrophages) as true class labels in both the MCA-spleen and MCA-lung data sets [10] (Table 2). The UMAP dimension reduction for the immune cell types and gene expression of true labels ...
plot2=LabelPoints(plot = plot1, points = top20, repel = TRUE) plot2 主成分碎石图可视化 sce = RunPCA(object = sce, do.print = FALSE) # 可视化 ElbowPlot(sce) VizDimLoadings(sce, dims = 1:5, reduction = "pca", nfeatures = 10) JackStrawPlot(sce,dims = 1:20, reduction = "pca"...
The "FindNeighbors" and "FindClusters" were harnessed for cell aggregation assessment. The k-nearest neighbor graph was developed by the "FindNeighbors" to determine each cell's closest neighbors. TSNE was then executed via the "RunTSNE" function. Cell markers from the CellMarker website (http...
接着,我们来看另外一篇在CSC上的综述文章,题目也差不多,Single-Cell Transcriptomics Meets Lineage Tracing 老规矩,还是先介绍文章的通讯作者 Van Oudenaarden这是在荷兰的一个研究组,名称很霸气呀, 定量生…
Identify cell type based on cell markers for single cell squencing 10stars4forksBranchesTagsActivity Star Notifications BranchesTags Folders and files Name Last commit message Last commit date Latest commit guokai8 Merge pull request#1from emontele/master ...
得到均一化之后的matrix之后: Biological analysis:Clustering 、Feature selection、Pseudotime analysis、Imputation、DE Seurat:Create seurat object、Normalization、Highly variable genes、dealing with confounders、linear dimensionality reduction、significant PCs、clustering cells、markers genes ...
Cells were clustered based on their expression profile, and cell types were annotated based on established cell markers available on LungMap9(https://lungmap.net/), CellMarker10, The Human Protein Atlas11(http://www.proteinatlas.org), and in the published literature (Fig.2a; Supplementary Dat...
Recent advances in single-cell technologies have enabled high-throughput molecular profiling of cells across modalities and locations. Single-cell transcriptomics data can now be complemented by chromatin accessibility, surface protein expression, adapti