bcRep: Advanced Analysis of B Cell Receptor Repertoire Data

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

Author
Julia Bischof
Date of publication
2016-06-06 09:20:14
Maintainer
Julia Bischof <Julia.Bischof@uksh.de>
License
GPL-2
Version
1.3.5

View on CRAN

Man pages

aaDistribution
Amino acid distribution of sequences
aaseqtab
Summary of amino acid sequences of B cells of one individual
aaseqtab2
Summary of amino acid sequences of B cells of another...
bcRep-package
Advanced Analysis of B Cell Receptor Repertoire Data
clones
Grouping sequences into clones
clones.allind
B cell clones of 8 individuals
clones.CDR3Length
CDR3 length distribution of clones
clones.filterFunctionality
Filter for productive/unproductive clones
clones.filterJunctionFrame
Filter for in-frame/out-of-frame clones
clones.filterSize
Filter clones for their size
clones.giniIndex
Gini index of clones
clones.ind
Data frame: clones of one individual
clones.shared
Shared clones between samples
combineIMGT
Combination of several IMGT output folders
compare.aaDistribution
Compare amino acid distribution of different samples
compare.geneUsage
Compare gene usage of different samples
compare.trueDiversity
Compare richness or diversity of different samples
dist.PCoA
Principal coordinate analysis (PCoA; multidimensional scaling...
geneUsage
Gene usage statistics
geneUsage.distance
Dissimilarity/distance indices for gene usage data
mutationtab
Summary of mutations cells
ntseqtab
Summary of nucleotide sequences of B cells of one individual
plotClonesCopyNumber
Copy number of clones
readIMGT
Read IMGT/HighV-QUEST output files
sequences.distance
Dissimilarity/distance indices for sequence data
sequences.functionality
Summary of functionality of sequences
sequences.geneComb
Gene/gene combinations
sequences.getAnyFunctionality
Filter for productive or unproductive sequences
sequences.getAnyJunctionFrame
Filter for in-frame or out-of-frame sequences
sequences.junctionFrame
Summary of junction frames of sequences
sequences.mutation
Basic statistics on mutations of sequences
sequences.mutation.AA
Detect amino acid mutations in V-, FR- or CDR-regions
sequences.mutation.base
Statistics about silent mutations
summarytab
Summary information of B cells of one individual
trueDiversity
True diversity of sequences
vgenes
VH gene usage data

Files in this package

bcRep
bcRep/inst
bcRep/inst/doc
bcRep/inst/doc/NEWS.pdf
bcRep/inst/doc/vignette.Rmd
bcRep/inst/doc/vignette.R
bcRep/inst/doc/vignette.html
bcRep/inst/NEWS.Rmd
bcRep/NAMESPACE
bcRep/data
bcRep/data/ntseqtab.rda
bcRep/data/aaseqtab2.rda
bcRep/data/summarytab.rda
bcRep/data/vgenes.rda
bcRep/data/datalist
bcRep/data/aaseqtab.rda
bcRep/data/clones.allind.rda
bcRep/data/clones.ind.rda
bcRep/data/mutationtab.rda
bcRep/R
bcRep/R/combineIMGT.R
bcRep/R/sequences.getAnyJunctionFrame.R
bcRep/R/compare.aaDistribution.R
bcRep/R/plotCompareGeneUsage.R
bcRep/R/sequences.functionality.R
bcRep/R/sequences.mutation.AA.R
bcRep/R/clones.filterJunctionFrame.R
bcRep/R/sequences.geneComb.R
bcRep/R/plotAADistribution.R
bcRep/R/aaDistribution.R
bcRep/R/geneUsage.distance.R
bcRep/R/clones.shared.summary.R
bcRep/R/plotCompareTrueDiversity.R
bcRep/R/clones.CDR3Length.R
bcRep/R/plotTrueDiversity.R
bcRep/R/sequences.getUnproductives.R
bcRep/R/sequences.getAnyFunctionality.R
bcRep/R/plotGeneUsage.R
bcRep/R/clones.shared.R
bcRep/R/plotClonesCDR3Length.R
bcRep/R/plotClonesCopyNumber.R
bcRep/R/trueDiversity.R
bcRep/R/plotSequencesMutationBase.R
bcRep/R/sequences.getOutOfFrames.R
bcRep/R/readIMGT.R
bcRep/R/clones.filterSize.R
bcRep/R/clones.filterFunctionality.R
bcRep/R/sequences.getProductives.R
bcRep/R/dist.PCoA.R
bcRep/R/sequences.getInFrames.R
bcRep/R/sequences.distance.R
bcRep/R/plotDistPCoA.R
bcRep/R/geneUsage.R
bcRep/R/plotSequencesMutationAA.R
bcRep/R/sequences.mutation.R
bcRep/R/sequences.junctionFrame.R
bcRep/R/compare.trueDiversity.R
bcRep/R/clones.giniIndex.R
bcRep/R/sequences.mutation.base.R
bcRep/R/plotGeneComb.R
bcRep/R/plotCompareAADistribution.R
bcRep/R/clones.R
bcRep/R/compare.geneUsage.R
bcRep/vignettes
bcRep/vignettes/vignette.Rmd
bcRep/MD5
bcRep/build
bcRep/build/vignette.rds
bcRep/DESCRIPTION
bcRep/man
bcRep/man/geneUsage.Rd
bcRep/man/clones.ind.Rd
bcRep/man/compare.aaDistribution.Rd
bcRep/man/clones.filterFunctionality.Rd
bcRep/man/mutationtab.Rd
bcRep/man/aaseqtab2.Rd
bcRep/man/clones.shared.Rd
bcRep/man/compare.trueDiversity.Rd
bcRep/man/readIMGT.Rd
bcRep/man/aaseqtab.Rd
bcRep/man/sequences.junctionFrame.Rd
bcRep/man/clones.giniIndex.Rd
bcRep/man/clones.allind.Rd
bcRep/man/clones.Rd
bcRep/man/sequences.functionality.Rd
bcRep/man/sequences.distance.Rd
bcRep/man/sequences.getAnyFunctionality.Rd
bcRep/man/aaDistribution.Rd
bcRep/man/sequences.geneComb.Rd
bcRep/man/dist.PCoA.Rd
bcRep/man/compare.geneUsage.Rd
bcRep/man/combineIMGT.Rd
bcRep/man/plotClonesCopyNumber.Rd
bcRep/man/sequences.mutation.AA.Rd
bcRep/man/clones.filterJunctionFrame.Rd
bcRep/man/ntseqtab.Rd
bcRep/man/sequences.mutation.Rd
bcRep/man/sequences.mutation.base.Rd
bcRep/man/clones.filterSize.Rd
bcRep/man/summarytab.Rd
bcRep/man/trueDiversity.Rd
bcRep/man/geneUsage.distance.Rd
bcRep/man/clones.CDR3Length.Rd
bcRep/man/bcRep-package.Rd
bcRep/man/sequences.getAnyJunctionFrame.Rd
bcRep/man/vgenes.Rd