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bcRep (version 1.3.4)

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

1.3.4

License

GPL-2

Maintainer

Julia Bischof

Last Published

April 26th, 2016

Functions in bcRep (1.3.4)

clones.filterJunctionFrame

Filter for in-frame/out-of-frame clones
clones.filterFunctionality

Filter for productive/unproductive clones
clones.giniIndex

Gini index of clones
clones.ind

Data frame: clones of one individual
sequences.mutation

Basic statistics on mutations of sequences
sequences.getAnyFunctionality

Filter for productive or unproductive sequences
compare.geneUsage

Compare gene usage of different samples
summarytab

Summary information of B cells of one individual
dist.PCoA

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

Summary of functionality of sequences
sequences.distance

Dissimilarity/distance indices for sequence data
trueDiversity

True diversity of sequences
sequences.getAnyJunctionFrame

Filter for in-frame or out-of-frame sequences
aaDistribution

Amino acid distribution of sequences
compare.aaDistribution

Compare amino acid distribution of different samples
sequences.mutation.AA

Detect amino acid mutations in V-, FR- or CDR-regions
clones.CDR3Length

CDR3 length distribution of clones
compare.trueDiversity

Compare richness or diversity of different samples
bcRep-package

Advanced Analysis of B Cell Receptor Repertoire Data
ntseqtab

Summary of nucleotide sequences of B cells of one individual
aaseqtab

Summary of amino acid sequences of B cells of one individual
combineIMGT

Combination of several IMGT output folders
plotClonesCopyNumber

Copy number of clones
clones.allind

B cell clones of 8 individuals
sequences.junctionFrame

Summary of junction frames of sequences
clones

Grouping sequences into clones
sequences.mutation.base

Base proportion nearby mutations
sequences.geneComb

Gene/gene combinations
vgenes

VH gene usage data
aaseqtab2

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

Read IMGT/HighV-QUEST output files
clones.shared

Shared clones between samples
mutationtab

Summary of mutations cells
geneUsage.distance

Dissimilarity/distance indices for gene usage data
geneUsage

Gene usage statistics
clones.filterSize

Filter clones for their size