##AnnData object with n_obs × n_vars=5992×36601# obs:'Clusters','_X','_Y'#var:'Accession','Chromosome','End','Start','Strand'# layers:'matrix','ambiguous','spliced','unspliced'sample_two=anndata.read_loom("/Users/linyu1/Desktop/bioinformation/End_analysis/velocyto/output_EU2.loom...
此教程展示了使用 scVelo 分析存储在 Seurat 对象中的 RNA 速率值。如果您在工作中使用 scVelo,请引用下文: Generalizing RNA velocity to transient cell states through dynamical modeling Volker Bergen, Marius Lange, Stefan Peidli, F. Alexander Wolf & Fabian J. Theis doi: https://doi.org/10.1101/8209...
转换为seurat对象 ldat<-ReadVelocity(file="~/Downloads/SCG71.loom")bm<-as.Seurat(x=ldat) 整合降维聚类 bm<-SCTransform(object=bm,assay="spliced")bm<-RunPCA(object=bm,verbose=FALSE)bm<-FindNeighbors(object=bm,dims=1:20)bm<-FindClusters(object=bm)bm<-RunUMAP(object=bm,dims=1:20) 速率...
But, before we do that, we will export all of the necessary meta-data from our Seurat object that is needed for our RNA Velocity object. This includes: Filtered Cell Ids UMAP or TSNE coordinates Clusters (Optional) Cluster Colors (Optional) ...
在上文中，我们定义了RNA velocity 为v(t)=dsdt=u(t)−γs(t)假设在t=0时刻，未剪接的mRNA...
(x=bm)show.velocity.on.embedding.cor(emb=Embeddings(object=bm,reduction="umap"),vel=Tool(object=bm,slot="RunVelocity"),n=200,scale="sqrt",cell.colors=ac(x=cell.colors,alpha=0.5),cex=0.8,arrow.scale=3,show.grid.flow=TRUE,min.grid.cell.mass=0.5,grid.n=40,arrow.lwd=1,do.par=FALSE...
object = bm, dims = 1:20)速率分析及可视化 bm <- RunVelocity(object = bm, deltaT = 1, kCells = 25, fit.quantile = 0.02)ident.colors <- (sc ales::hue_pal())(n = length(x = levels(x = bm)))names(x = ident.colors) <- levels(x = bm)cell.colors <- ident.co ...
show.velocity.on.embedding.cor(emb = Embeddings(object = bm, reduction ="umap"), vel = Tool(object = bm, slot ="RunVelocity"), n = 200, scale ="sqrt", cell.colors = ac(x = cell.colors, alpha = 0.5), cex = 0.8, arrow.scale = 3, show.grid.flow = TRUE, min.grid.cell.mas...
在上文中，我们定义了RNAvelocity为\boldsymbol{v}(t)=\frac{\mathrm{d} s}{\mathrm{~d} t}=u...
此教程展示了使用 scVelo 分析存储在 Seurat 对象中的 RNA 速率值。如果您在工作中使用 scVelo,请引用下文: Generalizing RNA velocity to transient cell states through dynamical modeling Volker Bergen, Marius Lange, Stefan Peidli, F. Alexander Wolf & Fabian J. Theis ...