The pseudotime trajectory
Webb1、细胞轨迹构建. 当 Monocle 对单细胞进行排序时，能够轻松地进行可视化和解释。. 如下图为对细胞排序后在二维空间中的轨迹。. 横纵坐标分别为两个主成分，图中每个圆点代 … Webb10 apr. 2024 · And the trajectory analysis was performed using the Monocle3 package to reveal the cell-state transitions. The DEGs changed along with the pseudotime were identified using the graph_test function in Monocle2. Analysis of bulk RNA-seq data
The pseudotime trajectory
Did you know?
Webb22 feb. 2024 · 而将细胞根据这个过程进行排序而形成一个轨迹，从而追踪伴随轨迹的过程变化函数，称之为“pseudotime”。 伪时间是一个抽象的分化单位：它只是一个细胞到轨迹起点的距离，沿着最短路径测量。 Monocle的微分分析工具包来查找在轨迹过程中受到调控的基因，如查找作为伪时间函数变化的基因，而“分支”表示随着轨迹进行，受到调控的基因有 … WebbThe name of a feature to use for colouring the cells. The pseudotime from the root of the trajectory to the cells as a named numeric vector. Source of the feature expression, …
WebbFinally, pseudotime trajectory inference showed that T-bet-expressing hyperactivated and proliferating memory B-cell populations were located at the terminal end of two trajectories, in both HIV-1 and HIV-2 infections. As the treatment-naïve aviremic HIV-2-infected individuals, ... WebbFinally, pseudotime trajectory inference showed that T-bet-expressing hyperactivated and proliferating memory B-cell populations were located at the terminal end of two …
WebbDefining pseudotime #. The first step in identifying the lineage structure of this data is to compute a diffusion map of the underlying nearest neighbors graph. sc.tl.diffmap will … WebbThis continuum trajectory or ‘pseudotime’, may reveal the developmental pathway and provide us with information on dynamic transcriptomic changes and other biological …
Webb15 Pseudotime Cell Trajectories ANALYSIS OF SINGLE CELL RNA-SEQ DATA 15 Pseudotime Cell Trajectories Comparison: Cell Trajectories Diffusion maps for high …
Webb10 apr. 2024 · Also, scRNA-Seq can facilitate the prediction of a theoretical lineage trajectory along a pseudotime scale to uncover the molecular programs that drive developmental processes. This is because it can reveal the gene expression profiles of both the steady and transitioning states of captured cells. lyons crew by jordan silverWebb29 mars 2024 · Green dot indicates supervised pseudotime root. Black lines represent putative cell fate trajectories. (C) Expression of genes associated with each phase of the cell cycle were labeled on UMAP. (D) Pseudotime projections of cells from untreated controls or mice with EoE or ESCC. Lines indicate predicted trajectories with trajectory … lyons creek middle school gradeWebb7 juli 2024 · A unique aspect of scRNA-Seq data is the ability to extract detailed dynamics even when using a small number, or a single, time point. Such analysis, which is often termed pseudotime ordering of cells results in a reconstructed trajectory of cells along a (usually small) number of branches and paths. lyonscsd.orgWebbIn classical mechanics, a trajectory is defined by Hamiltonian mechanics via canonical coordinates; hence, a complete trajectory is defined by position and momentum, simultaneously. The mass might be a projectile or a satellite. [1] For example, it can be an orbit — the path of a planet, asteroid, or comet as it travels around a central mass . lyons creek middle school mapWebb1 apr. 2024 · Trying to analyse cells every 10 seconds can be pretty tricky, so ‘pseudotime’ analysis takes a single sample and assumes that those cells are all on slightly different points along a path of differentiation. Some cells might be slightly more mature and others slightly less, all captured at the same ‘time’. lyons creek road niagara fallsWebbTrajectory analysis. The monocle2 was used and in-house R scripts to conduct pseudotime analysis for hippocampus, heart, liver, and kidney. The recommended analysis protocol was followed, except using FindMarkers function from Seurat package to perform pairwise comparison across different conditions to find the statistically significant up- and down … lyons crest homes garland txWebbUsing a dynamical systems approach and RNA velocity, we find that aged MuSCs follow the same differentiation trajectory as young cells but stall in differentiation near a commitment decision. Our results suggest that differentiation reveals latent features of aging and that fate commitment decisions are delayed in aged myogenic cells in vitro. lyons cricketer