# Analysis Tools for 10X V(D)J Data

## Documentation for package ‘VDJdive’ version 1.11.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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