Analysis Tools for 10X V(D)J Data

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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