WebNov 8, 2024 · orderCells() will then "walk" along the trajectory, and as it encounters additional cells, it will assign them increasingly large values of Pseudotime. Value an … WeborderCells: Orders cells according to pseudotime. order_p_node: Return an ordering for a P node in the PQ tree; package-deprecated: Plots the minimum spanning tree on cells. This …
monocle: Clustering, differential expression, and trajectory …
Webcds2 <-reduceDimension (cds2, max_components = 2) cds2 <-orderCells (cds2) plot_cell_trajectory (cds2, color_by = "Stage") We clearly get a very different trajectory with the negative binomial, no branching of the blastocyst stage. Test instead with using top dispersed genes for pseudotime ordering. WebMar 29, 2024 · 拟时分析. 拟时(pseudotime)分析,又称细胞轨迹(cell trajectory)分析,通过拟时分析可以推断出发育过程细胞的分化轨迹或细胞亚型的演化过程,在发育相关 … d4 waypoints
orderCells()函数报错问题——修改后monocle2包 - 知乎
WebA SingleCellExperiment object of the data has been provided with the tradeSeq package and can be retrieved as shown below. The data and UMAP reduced dimensions were derived from following the Monocle 3 vignette. The main vignette focuses on using tradeSeq downstream of slingshot. Here, we present how to use tradeSeq downstream of monocle … Webcds <-reduceDimension (cds, max_components = 2) #Now that the space is reduced, it???s time to order the cells using the orderCells function as shown below. cds <-orderCells … bing photo identifier