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