SATIJALAB . ORG {}

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Keywords {🔍}

cells, features, seurat, pbmc, data, feature, dataset, pca, function, plot, expression, pcs, clusters, cluster, object, number, cell, true, genes, set, reduction, markers, clustering, based, default, dims, matrix, analysis, results, metrics, highly, downstream, datasets, positive, cda, count, top, negative, ilr, find, pct, fcgra, gene, variable, mitochondrial, counts, visualize, step, expressed, msa,

Topics {✒️}

scrna-seq data [snn-cliq standard pre-processing workflow highly interconnected ‘quasi-cliques visualize feature-feature relationships /data/pbmc3k/filtered_gene_bc_matrices/hg19/ graph-based clusters determined graph-based clustering approach low-quality cells visualize qc metrics low-dimensional space standard modularity function scrna-seq data principle components based k-nearest neighbor dimensional reduction techniques linear dimensional reduction exhibit high cell unique molecular identified remove unwanted sources highly variable features adversely affect results highlight biological signal extensive technical noise highly-expressed genes qc metrics commonly increased values leading qc metrics stored place similar cells variance relationship inherent pc essentially representing top principal components feature expression measurements visualizes feature expression removing unwanted cells iteratively group cells knn graph based performing downstream analyses low p-values previously identified pcs unique feature counts test argument requires statistical test based previously defined dimensionality suggest exploring ridgeplot determine relevant sources resampling test inspired roc test returns correlated feature set dimension reduction plots genes cell doublets

Questions {❓}

• How can I remove unwanted sources of variation, as in Seurat v2?
• However, how many componenets should we choose to include?
• What does data in a count matrix look like?
• Where are QC metrics stored in Seurat?

External Links {🔗}(11)

• What's the income of https://s3-us-west-2.amazonaws.com/10x.files/samples/cell/pbmc3k/pbmc3k_filtered_gene_bc_matrices.tar.gz?
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