Man pages for kstreet13/VDJdive
Analysis Tools for 10X V(D)J Data
| abundanceVDJ | Create an abundance graph for clonotype expansion |
| addVDJtoSCE | Add 10X CellRanger V(D)J data to SingleCellExperiment |
| barVDJ | Create a bar graph for clonotype expansion |
| boxVDJ | Create a box plot for diversity measures |
| calculateDiversity | Sample diversity estimation |
| clonoStats | Assign cell-level clonotypes and calculate abundances |
| clonoStats-class | 'clonoStats' object class |
| contigs | SplitDataFrameList containing AIRR-seq (TCR) data for six... |
| pieVDJ | Create a pie chart for clonotype expansion |
| readVDJcontigs | Load 10X CellRanger V(D)J data |
| runBreakaway | Clonotype richness estimation with Breakaway |
| runVDJPCA | Run PCA on clonotype abundance matrix |
| scatterVDJ | Create a scatterplot for diversity evenness and abundance |
| splitClonotypes | Split cell-level clonotype counts by sample |
| summarizeClonotypes | Get sample-level clonotype counts |
| writeVDJcontigs | Write V(D)J contig data in 10X format |
