# Advanced Analysis of B Cell Receptor Repertoire Data

## Documentation for package ‘bcRep’ version 1.3.6

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

## Help Pages

bcRep-package | Advanced Analysis of B Cell Receptor Repertoire Data
aaDistribution | Amino acid distribution of sequences
aaseqtab | Summary of amino acid sequences of B cells of one individual
aaseqtab2 | Summary of amino acid sequences of B cells of another individual
bcRep | Advanced Analysis of B Cell Receptor Repertoire Data
clones | Grouping sequences into clones
clones.allind | B cell clones of 8 individuals
clones.CDR3Length | CDR3 length distribution of clones
clones.filterFunctionality | Filter for productive/unproductive clones
clones.filterJunctionFrame | Filter for in-frame/out-of-frame clones
clones.filterSize | Filter clones for their size
clones.giniIndex | Gini index of clones
clones.IDlist | Match sequence ID's and clone ID's
clones.ind | Data frame: clones of one individual
clones.shared | Shared clones between samples
clones.shared.summary | Shared clones between samples
combineIMGT | Combination of several IMGT output folders
compare.aaDistribution | Compare amino acid distribution of different samples
compare.geneUsage | Compare gene usage of different samples
compare.trueDiversity | Compare richness or diversity of different samples
dist.PCoA | Principal coordinate analysis (PCoA; multidimensional scaling [MDS]) of dissimilarity/distance indices
geneUsage | Gene usage statistics
geneUsage.distance | Dissimilarity/distance indices for gene usage data
mutationtab | Summary of mutations cells
ntseqtab | Summary of nucleotide sequences of B cells of one individual
plotAADistribution | Amino acid distribution of sequences
plotClonesCDR3Length | CDR3 length distribution of clones
plotClonesCopyNumber | Copy number of clones
plotCompareAADistribution | Compare amino acid distribution of different samples
plotCompareGeneUsage | Compare gene usage of different samples
plotCompareTrueDiversity | Compare richness or diversity of different samples
plotDistPCoA | Principal coordinate analysis (PCoA; multidimensional scaling [MDS]) of dissimilarity/distance indices
plotGeneComb | Gene/gene combinations
plotGeneUsage | Gene usage statistics
plotSequencesMutationAA | Detect amino acid mutations in V-, FR- or CDR-regions
plotSequencesMutationBase | Statistics about silent mutations
plotTrueDiversity | True diversity of sequences
readIMGT | Read IMGT/HighV-QUEST output files
sequences.distance | Dissimilarity/distance indices for sequence data
sequences.functionality | Summary of functionality of sequences
sequences.geneComb | Gene/gene combinations
sequences.getAnyFunctionality | Filter for productive or unproductive sequences
sequences.getAnyJunctionFrame | Filter for in-frame or out-of-frame sequences
sequences.getInFrames | Filter for in-frame or out-of-frame sequences
sequences.getOutOfFrames | Filter for in-frame or out-of-frame sequences
sequences.getProductives | Filter for productive or unproductive sequences
sequences.getUnproductives | Filter for productive or unproductive sequences
sequences.junctionFrame | Summary of junction frames of sequences
sequences.mutation | Basic statistics on mutations of sequences
sequences.mutation.AA | Detect amino acid mutations in V-, FR- or CDR-regions
sequences.mutation.base | Statistics about silent mutations
summarytab | Summary information of B cells of one individual
trueDiversity | True diversity of sequences
vgenes | VH gene usage data