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bcRep (version 1.2.2)

Advanced Analysis of B Cell Receptor Repertoire Data

Description

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

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Version

Install

install.packages('bcRep')

Monthly Downloads

29

Version

1.2.2

License

GPL-2

Maintainer

Julia Bischof

Last Published

October 28th, 2015

Functions in bcRep (1.2.2)

geneUsage

Gene usage of clones
clones.allind

B cell clones of 8 individuals
aaseqtab

Summary of amino acid sequences of B cells of one individual
compare.trueDiversity

Compare richness or diversity of different samples
combineIMGT

Combination of several IMGT output folders
clones.shared

Shared clones between individuals
sequences.functionality

Summary of functionality of sequences
sequences.geneComb

Gene combinations gene families
clones.ind

Data frame: clones of one individual
sequences.mutation

Basic statistics on mutations of sequences
compare.geneUsage

Compare gene usage of different samples
clones

Grouping sequences into clones
bcRep-package

Advanced Analysis of B Cell Receptor Repertoire Data
aaseqtab2

Summary of amino acid sequences of B cells of another individual
sequences.getAnyJunctionFrame

Filter for in-frame or out-of-frame sequences
sequences.junctionFrame

Summary of junction frames of sequences
clones.CDR3Length

CDR3 length distribution of clones
clones.filterSize

Filter clones for their size
ntseqtab

Summary of nucleotide sequences of B cells of one individual
readIMGT

Read IMGT/HighV-QUEST output files
clones.giniIndex

Gini index of clones
aaDistribution

Amino acid distribution of sequences
clones.filterFunctionality

Filter for productive/unproductive clones
mutationtab

Summary of mutations cells
trueDiversity

True diversity of sequences
sequences.getAnyFunctionality

Filter for productive or unproductive sequences
summarytab

Summary information of B cells of one individual
clones.filterJunctionFrame

Filter for in-frame/out-of-frame clones
plotClonesCopyNumber

Copy number of clones
compare.aaDistribution

Compare amino acid distribution of different samples