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bcRep (version 1.3.1)

Advanced Analysis of B Cell Receptor Repertoire Data

Description

Methods for advanced analysis of B cell receptor repertoire data, like gene usage, mutations, clones, diversity, distance measures and multidimensional scaling and their visualisation.

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Version

Install

install.packages('bcRep')

Monthly Downloads

29

Version

1.3.1

License

GPL-2

Maintainer

Julia Bischof

Last Published

February 25th, 2016

Functions in bcRep (1.3.1)

aaDistribution

Amino acid distribution of sequences
aaseqtab

Summary of amino acid sequences of B cells of one individual
clones.filterJunctionFrame

Filter for in-frame/out-of-frame clones
sequences.mutation.AA

Detect amino acid mutations in V-, FR- or CDR-regions
geneUsage.distance

Dissimilarity/distance indices for gene usage data
geneUsage

Gene usage statistics
sequences.functionality

Summary of functionality of sequences
aaseqtab2

Summary of amino acid sequences of B cells of another individual
summarytab

Summary information of B cells of one individual
clones.allind

B cell clones of 8 individuals
compare.geneUsage

Compare gene usage of different samples
clones.ind

Data frame: clones of one individual
combineIMGT

Combination of several IMGT output folders
sequences.getAnyFunctionality

Filter for productive or unproductive sequences
sequences.mutation.base

Base proportion nearby mutations
compare.trueDiversity

Compare richness or diversity of different samples
readIMGT

Read IMGT/HighV-QUEST output files
mutationtab

Summary of mutations cells
sequences.distance

Dissimilarity/distance indices for sequence data
ntseqtab

Summary of nucleotide sequences of B cells of one individual
clones.CDR3Length

CDR3 length distribution of clones
clones.filterFunctionality

Filter for productive/unproductive clones
clones.shared

Shared clones between samples
vgenes

VH gene usage data
sequences.junctionFrame

Summary of junction frames of sequences
clones.filterSize

Filter clones for their size
bcRep-package

Advanced Analysis of B Cell Receptor Repertoire Data
trueDiversity

True diversity of sequences
sequences.getAnyJunctionFrame

Filter for in-frame or out-of-frame sequences
clones.giniIndex

Gini index of clones
dist.PCoA

Principal coordinate analysis (PCoA; multidimensional scaling [MDS]) of dissimilarity/distance indices
clones

Grouping sequences into clones
plotClonesCopyNumber

Copy number of clones
sequences.mutation

Basic statistics on mutations of sequences
sequences.geneComb

Gene/gene combinations
compare.aaDistribution

Compare amino acid distribution of different samples