Skip to main content

Table 1 List of modules implemented in VDJView with their outputs and integrated packages

From: Exploring and analysing single cell multi-omics data with VDJView

ModuleDescriptionSoftware packagesOutput
FilteringSelection of cells based on metadata, gene and immune receptor featuresdplyrVenn Diagram, data-table
Quality controlMetrics with options for easily filtering cells according to total read counts, number of genes, and percentage of mitochondrial/ribosomal genesSeurat [11]Violin plots
Random samplingSelection of small subsets of data, providing the ability to analyse larger datasetsSeurat 
Clonotype usagePie charts of single- and paired-chain CDR3 contig usage for both T and B cells. Tables detailing single- and paired-chain CDR3 contigs generated across all cellsplotlyPie charts, data-tables
CDR3 lengthDistribution of CDR3 lengths for single- and paired chainstcRHistograms
VDJ gene usageDistribution of V, D and J gene usage for single chainstcRHistograms
Gene interactionsFrequencies of inter- and intra-chain VDJ gene pairings, and inter-chain CDR3 pairingsRcircos [12]Circos plots
Shared clonotypesTable and scatter plot detailing the number of single- and paired-chain CDR3 contigs and VDJ genes that occur in multiple subgroups, and their frequency in each grouptcRScatter plot, data-table
Dimensionality reductionPCA plot, t-SNE plot and UMAP plot with customisable parameters. Metadata can be used to control data point shape, size and colour. Data points are selectable and displayed with their metadata in a data-table below each plotScater [13], Seurat, SC3 [14]PCA plots, t-SNE plots, UMAP plots, data-tables
Unsupervised clusteringConsensus matrix, gene expression heatmaps and marker-gene heatmaps are calculated by SC3 based on user defined cluster ranges, p-values and AUROC values. Metadata can be displayed above plot. Gene list can be uploaded to generate an expression heatmap. Tabular SC3 clustering information is generatedScater, SC3Consensus matrix, Expression matrix, DE Genes heatmap, Marker genes heatmap, data-table
Supervised clusteringDifferentially expressed gene heatmap generated by MAST comparing groups of cells based on clusters predetermined by the user, p-value and fold change thresholds. Gene fold change values and a tabular version of the heatmap are generatedMAST [15], Scater, pheatmapGene expression matrix, data-tables
Pseudo-timePseudo-time plot to determine single-cell state trajectories based on genes which are differentially expressed between user defined metadata groupsMonocle [16]Pseudo-time cell trajectory plot
Cell metadata summaryTabular summary of the cells uploaded, the metadata associated with them and the number of receptors contigs, and expressed genes reported for each cell Data-table