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What is the resolution parameter for seurats findclusters?
In Seurats ‘ documentation for FindClusters () function it is written that for around 3000 cells the resolution parameter should be from 0.6 and up to 1.2. I am wondering then what should I use if I have 60 000 cells?
How is the stability index calculated in Seurat?
Have a look into clustree, to assess the different clusters by clustering them and see different levels The stability index from the SC3 package (Kiselev et al. 2017) measures the stability of clusters across resolutions and is automatically calculated when a clustering tree is built.
When to experiment with selection parameters in Seurat?
The usefulness of the clustering will very much depend on the selection of variable genes, therefore, depending on the (diversity of the) dataset, you will want to experiment with selection parameters or subset the dataset and repeat the above procedure. That is a very general recommendation.
How to use Seurat for graph clustering in archr?
We have had the most success using the graph clustering approach implemented by Seurat. In ArchR, clustering is performed using the addClusters () function which permits additional clustering parameters to be passed to the Seurat::FindClusters () function via ….
How to cluster single cell chromatin accessibility in Seurat?
5.1 Clustering using Seurat’s FindClusters () function | ArchR: Robust and scaleable analysis of single-cell chromatin accessibility data. We have had the most success using the graph clustering approach implemented by Seurat.
Which is a useful feature of Seurat v2.0?
A useful feature in Seurat v2.0 is the ability to recall the parameters that were used in the latest function calls for commonly used functions. For FindClusters, we provide the function PrintFindClustersParams to print a nicely formatted summary of the parameters that were chosen.
What does a positive value on Seurat mean?
Positive values indicate that the gene is more highly expressed in the first group #’ the total number of genes in the dataset. Other correction methods are not #’ the number of tests performed.
What are the statistics in Seurat generics.r?
#’ statistics as columns (p-values, ROC score, etc., depending on the test used (\\code {test.use})). The following columns are always present: #’ \\item \\code {avg_logFC}: log fold-chage of the average expression between the two groups. Positive values indicate that the gene is more highly expressed in the first group