SATIJALAB . ORG {
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Title:
Analysis, visualization, and integration of Visium HD spatial datasets with Seurat • Seurat
Description:
Seurat
Website Age:
10 years and 11 months (reg. 2014-07-30).
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Keywords {🔍}
cells, features, seurat, dataset, data, plot, pbmc, feature, cell, cluster, function, expression, clusters, pca, reduction, object, genes, true, number, analysis, markers, variable, default, positive, pcs, clustering, matrix, based, metrics, users, downstream, datasets, techniques, negative, count, gene, results, counts, standard, highly, set, dimensional, dims, ilr, cda, find, umap, pct, single, preprocessing,
Topics {✒️}
/brahms/mollag/practice/filtered_gene_bc_matrices/hg19/ scrna-seq data [snn-cliq standard pre-processing workflow highly interconnected ‘quasi-cliques graph-based clustering approach visualize feature-feature relationships graph-based clusters determined linear dimensional reduction low-dimensional space visualize qc metrics dimensional reduction techniques highlight biological signal low-quality cells scrna-seq analysis scrna-seq data vignettes/pbmc3k_tutorial developed alternative workflows extensive technical noise determine relevant sources k-nearest neighbor unique molecular identified global-scaling relies remove unwanted sources exhibit high cell features = top10$gene standard modularity function highly-expressed genes feature expression measurements visualizes feature expression highly variable features principle components based adversely affect results qc metrics commonly computationally expensive procedure place similar cells dimension reduction plots qc metrics stored correlated feature set removing unwanted cells variance relationship inherent iteratively group cells learn underlying structure knn graph based single cell preprocessing repeat downstream analyses performing downstream analyses unique feature counts /output/images/pbmc3k_umap suggest exploring ridgeplot previously identified pcs
Questions {❓}
- For users who are not using presto, you can examine the documentation for this function (?
- However, how many components should we choose to include?
- What does data in a count matrix look like?
- Where are QC metrics stored in Seurat?
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Analytics and Tracking {📊}
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