Analysis Tools for 10X V(D)J Data


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Documentation for package ‘VDJdive’ version 1.0.0

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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