The pseudotime trajectory
WebbTrajectory 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 … Webb11 apr. 2024 · Pseudotime analysis of single cells. Pseudotime trajectory analysis in keratinocytes was generated using R package Monocle (version 2.18.0) [25]. Cells were …
The pseudotime trajectory
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Webb12 apr. 2024 · In addition, pseudotime trajectory analysis was applied to evaluate the adverse effect of DEHP on PTM development (Fig. 5 H–I and Figs. S7B–D). The PTMs in the DEHP exposure group were spread evenly along the trajectory, while those in the control group were distributed mainly in states 1, 2 and 4. Webb5 apr. 2024 · Pseudotime trajectory analysis confirmed that the cell arrangement on the pseudotime line was CSCs and EPCs to CAFs, and 2111 genes were defined as state 2 …
Webb2 aug. 2024 · Pseudotime is a latent (unobserved) dimension that measures the cells’ advancement through the transition. Is related to but not necessarily the same as an experimental capture time; instead, it is a proxy for the actual time. Mathematically, it is the geodesic distance of the cells from a single or set of progenitor (s)/root node (s). WebbWe constructed single-cell development and differentiation trajectory in the pseudotime analysis using the Monocle 2 package (version 2.6.4; Monocle, USA). 21 We used the normalized expression cells × genes matrix to create a starting subject CellDataSet class. 22 We used the differentialGeneTest function to identify specific genes across multiple …
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 … Webb8 apr. 2024 · Using single-cell RNA sequencing techniques, Monocle pseudotime trajectory and CellphoneDB analysis, we demonstrate that the stiffness of the hydrogel alone does not influence the differentiation of NPCs, but the degradation of the hydrogel that enhances cell–cell interactions is possibly the main reason.
Webb5 apr. 2024 · Stemness-related pseudotime trajectory analysis The single-cell pseudotime trajectory of CSCs, epithelial cells (EPCs), and cancer-associated fibroblasts (CAFs) was established using the algorithm of Monocle 2. Single cells were projected onto a space, forming a trajectory with branch points.
Webbstlearn.spatial.trajectory.pseudotime¶. Next Previous. © Copyright 2024, Genomics and Machine Learning lab Revision 89abaa9b. birth security paperWebbJiang et al. provide a single-cell transcriptomic census of the cynomolgus macaque placenta during gestation and bioinformatic evidence for stage-related features of cells at the maternal-fetal interface, the potential origin of placenta villous core cells, and the cross-species maternal-fetal features of macaques. They also present a comparison with data … birth secret korean dramaWebb29 apr. 2024 · However, existing methods do not account for pseudotime inference uncertainty, and they have either ill-posed p-values or restrictive models. ... Pseudotime … birth senility illness and deathWebbPseudotime and Trajectory Inference . Stefania Giacomello The basics . Cells display a continuous spectrum of states (i.e. activation and/ or differentiation process) Individual … dargavel primary school jobsWebbTrajectory Inference with VIA. VIA is a single-cell Trajectory Inference method that offers topology construction, pseudotimes, automated terminal state prediction and automated … dargavel primary school bishopton addressWebb12 maj 2024 · Pseudotime trajectory constructed by other algorithms. To check whether other algorithms can provide solutions to construct cell developmental pathways, we combined their transformed count matrix with Monocle to build the pseudotime trajectory from scATAC-seq data. A similar preprocessing method was applied to ensure the … birth see baby actualy come outWebbDefining 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 … dargavel primary school badge