single cell Davo October 1, 2017 15. na: logical. The result from Monocle 2 here also shows two main branches. We use the slingshot package (Street et al. Running Diffusion Pseudotime. Trajectory Analysis with Diffusion Pseudotime - Danh Truong, PhD We will make use of the slingshot package proposed in (Street et al. Perform the first steps of the analysis. First, download the dataset from github within your Terminal tab as on Day 1: Then, within R, import the rds file. The progenitor or precursor cells of each lineage were enclosed in frames of dashed lines. Single-cell RNA-seq. This may be useful if you have multiple time points, or a pseudotime trajectory. less. Cells that were identified as being specific to Lineage 2 will have NA values for slingPseudotime_1, but they will have real values for slingPseudotime_2. We will regress each gene on the pseudotime variable we have generated, using a general additive model (GAM). Slingshot was designed to model developmental trajectories in single-cell RNA sequencing data and serve as a component in an analysis pipeline after dimensionality reduction and clustering. Calculate pseudotime and lineages with Slingshot. Trajectory analysis - Single cell transcriptomics I am doing scRNA-Seq analysis, and I am doing RNA velocity and pseudotime analyses as part of my analysis pipeline. slingPseudotime : Get Slingshot pseudotime values 轨迹推断也常被称作“伪时间分析”（pseudotime analysis）。. Often called pseudotime, but doesn’t have to relate to cells in different times in a process (could be spatial differences). Be aware that Slingshot does not provide information on the direction of development, but merely a tree topology. TSCAN is an R package to support in silico reconstruction of cells’ pseudotime. This chapter introduces how to apply TSCAN to scRNA-seq data to perform pseudotime analysis. Randomly splits the SingleCellExperiment object into that number of bins and runs slingshot on each bin. We will regress each gene on the pseudotime variable we have generated, using a general additive model (GAM). Trajectory inference - Wikipedia pseudotime Hi, I am doing RNA velocity and pseudotime analyses on my single-cell RNA-Seq datasets.
