Learn R Programming

bcRep (version 1.3.6)

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.

Copy Link

Version

Install

install.packages('bcRep')

Monthly Downloads

57

Version

1.3.6

License

GPL-2

Maintainer

Julia Bischof

Last Published

December 19th, 2016

Functions in bcRep (1.3.6)

compare.geneUsage

Compare gene usage of different samples
clones.shared

Shared clones between samples
geneUsage.distance

Dissimilarity/distance indices for gene usage data
compare.trueDiversity

Compare richness or diversity of different samples
clones

Grouping sequences into clones
bcRep-package

Advanced Analysis of B Cell Receptor Repertoire Data
compare.aaDistribution

Compare amino acid distribution of different samples
clones.IDlist

Match sequence ID's and clone ID's
dist.PCoA

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

Combination of several IMGT output folders
sequences.geneComb

Gene/gene combinations
plotClonesCopyNumber

Copy number of clones
sequences.getAnyJunctionFrame

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

Summary of nucleotide sequences of B cells of one individual
sequences.functionality

Summary of functionality of sequences
clones.ind

Data frame: clones of one individual
sequences.distance

Dissimilarity/distance indices for sequence data
geneUsage

Gene usage statistics
mutationtab

Summary of mutations cells
readIMGT

Read IMGT/HighV-QUEST output files
sequences.mutation.AA

Detect amino acid mutations in V-, FR- or CDR-regions
sequences.getAnyFunctionality

Filter for productive or unproductive sequences
summarytab

Summary information of B cells of one individual
sequences.junctionFrame

Summary of junction frames of sequences
sequences.mutation

Basic statistics on mutations of sequences
sequences.mutation.base

Statistics about silent mutations
trueDiversity

True diversity of sequences
vgenes

VH gene usage data
clones.filterJunctionFrame

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

Gini index of clones
clones.filterSize

Filter clones for their size
aaseqtab

Summary of amino acid sequences of B cells of one individual
aaseqtab2

Summary of amino acid sequences of B cells of another individual
clones.allind

B cell clones of 8 individuals
aaDistribution

Amino acid distribution of sequences
clones.CDR3Length

CDR3 length distribution of clones
clones.filterFunctionality

Filter for productive/unproductive clones