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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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Install
install.packages('bcRep')
Monthly Downloads
104
Version
1.2.2
License
GPL-2
Maintainer
Julia Bischof
Last Published
October 28th, 2015
Functions in bcRep (1.2.2)
Search functions
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