Web2 days ago · “RunUMAP” function implemented in Seurat was used for dimensionality ... and Pseudotime trajectories (right) analysis of indicated germ cell types. Cells were ordered from beginning (darkest blue color) to end (lightest blue) as shown in the arrow. (C) Pseudotime trajectories analysis of indicated four germ cell types ... WebOct 1, 2024 · Getting started with Monocle. single cell Davo October 1, 2024 15. Monocle is an R package developed for analysing single cell gene expression data. Specifically, the package provides functionality for clustering and classifying single cells, conducting differential expression analyses, and constructing and investigating inferred …
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WebNov 18, 2024 · Overview. Asc-Seurat is a modular web application implemented using R language and user interface provided by the Shiny framework [] and R [].The main modules are described in Fig. 1 and encapsulate several analytical procedures including: (1) the algorithmic capabilities of Seurat for cell clustering, differential expression analysis, and … WebApr 5, 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-specific genes. There were 41 common genes obtained by taking intersection of the up-regulated genes with state 2-specific genes and the marker genes of CSCs, EPCs and … chevy dealers near fayetteville ar
Asc-Seurat: analytical single-cell Seurat-based web application
Web(F) Pseudotime was colored in a gradient from dark to light blue. The start of pseudotime is indicated by dark blue, the end of pseudotime by light blue (upper). Pseudotime trajectory of 6 subclusters was generated by Monocle2 (lower). (G) The key genes expression of immune checkpoint in 6 subclusters. (H) SCENIC analysis of 6 subclusters. WebOct 22, 2024 · To facilitate analysis or plotting using Spectre, or other generic tools (e.g. ggplot2, etc), Spectre provides a function for converting Seurat or SingleCellExperiment objects into a simple data.table.: Here we provide a brief tutorial on using Spectre's plotting, aggregation, and summary data functions on scRNAseq data. WebMay 14, 2024 · To identify distinct cell type populations and to directly compare cell type identity in the presence and absence of sucrose, we performed unsupervised clustering analysis of all 12,198 single cells with the canonical correlation analysis function of Seurat (Butler et al., 2024, Satija et al., 2015) (Figure 1 B; Figure S1 E).All 17 cell type clusters … chevy dealers near hershey