WebI am trying to dig deeper into my Seurat single-cell data analysis. If I want to further sub-cluster a big cluster then what would be the best way to do it: 1) Decreasing the resolution at FindClusters stage or 2) extracting the individual cell index and re-clustering and then further analysis. WebMay 15, 2024 · Seurat v3 also supports the projection of reference data (or meta data) onto a query object. While many of the methods are conserved (both procedures begin by identifying anchors), there are two important distinctions between data transfer and integration: In data transfer, Seurat does not correct or modify the query expression data.
How to combine clusters? · Issue #3277 · satijalab/seurat
WebTo perform the subclustering, there are a couple of different methods you could try. The easiest would be to run the FindNeighbors () and FindClusters () on the subsetted cells, … WebMar 23, 2024 · Seurat offers two workflows to identify molecular features that correlate with spatial location within a tissue. The first is to perform differential expression based on pre … cynthia bonner
r - Resolution parameter in Seurat
WebJan 9, 2024 · 1 Increase the clustering resolution parameter to generate more (smaller) clusters, see FindClusters in the Seurat docs. Whether or not this will neatly, split your clusters into subclusters depends on your data, but normally one can easily separate CD4 and NK cells from PBMCs. See also the Clustree approach for determining the optimal … WebSeurat uses a graph-based clustering approach, which embeds cells in a graph structure, using a K-nearest neighbor (KNN) graph (by default), with edges drawn between cells with similar gene expression patterns. WebApr 17, 2024 · Describes the standard Seurat v3 integration workflow, and applies it to integrate multiple datasets collected of human pancreatic islets (across different technologies). We also demonstrate how Seurat v3 can be used as a classifier, transferring cluster labels onto a newly collected dataset. We recommend this vignette for new users … cynthiaboone heavenlyescapesandtravels.com