bcRep: Advanced Analysis of B Cell Receptor Repertoire Data
Version 1.3.6

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

Browse man pages Browse package API and functions Browse package files

AuthorJulia Bischof
Date of publication2016-12-19 13:25:03
MaintainerJulia Bischof <Julia.Bischof@uksh.de>
LicenseGPL-2
Version1.3.6
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("bcRep")

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.IDlist: Match sequence ID's and clone ID's
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

Functions

aaDistribution Man page Source code
aaseqtab Man page
aaseqtab2 Man page
bcRep Man page
bcRep-package Man page
clones Man page Source code
clones.CDR3Length Man page Source code
clones.IDlist Man page Source code
clones.allind Man page
clones.filterFunctionality Man page Source code
clones.filterJunctionFrame Man page Source code
clones.filterSize Man page Source code
clones.giniIndex Man page Source code
clones.ind Man page
clones.shared Man page Source code
clones.shared.summary Man page Source code
combineIMGT Man page Source code
compare.aaDistribution Man page Source code
compare.geneUsage Man page Source code
compare.trueDiversity Man page Source code
dist.PCoA Man page Source code
geneUsage Man page Source code
geneUsage.distance Man page Source code
mutationtab Man page
ntseqtab Man page
plotAADistribution Man page Source code
plotClonesCDR3Length Man page Source code
plotClonesCopyNumber Man page Source code
plotCompareAADistribution Man page Source code
plotCompareGeneUsage Man page Source code
plotCompareTrueDiversity Man page Source code
plotDistPCoA Man page Source code
plotGeneComb Man page Source code
plotGeneUsage Man page Source code
plotSequencesMutationAA Man page Source code
plotSequencesMutationBase Man page Source code
plotTrueDiversity Man page Source code
readIMGT Man page Source code
sequences.distance Man page Source code
sequences.functionality Man page Source code
sequences.geneComb Man page Source code
sequences.getAnyFunctionality Man page Source code
sequences.getAnyJunctionFrame Man page Source code
sequences.getInFrames Man page Source code
sequences.getOutOfFrames Man page Source code
sequences.getProductives Man page Source code
sequences.getUnproductives Man page Source code
sequences.junctionFrame Man page Source code
sequences.mutation Man page Source code
sequences.mutation.AA Man page Source code
sequences.mutation.base Man page Source code
summarytab Man page
trueDiversity Man page Source code
vgenes Man page

Files

inst
inst/NEWS.pdf
inst/doc
inst/doc/NEWS.pdf
inst/doc/vignette.Rmd
inst/doc/vignette.R
inst/doc/vignette.html
inst/NEWS.Rmd
NAMESPACE
data
data/ntseqtab.rda
data/aaseqtab2.rda
data/summarytab.rda
data/vgenes.rda
data/datalist
data/aaseqtab.rda
data/clones.allind.rda
data/clones.ind.rda
data/mutationtab.rda
R
R/combineIMGT.R
R/sequences.getAnyJunctionFrame.R
R/compare.aaDistribution.R
R/plotCompareGeneUsage.R
R/sequences.functionality.R
R/sequences.mutation.AA.R
R/clones.filterJunctionFrame.R
R/sequences.geneComb.R
R/plotAADistribution.R
R/aaDistribution.R
R/geneUsage.distance.R
R/clones.shared.summary.R
R/plotCompareTrueDiversity.R
R/clones.CDR3Length.R
R/plotTrueDiversity.R
R/sequences.getUnproductives.R
R/sequences.getAnyFunctionality.R
R/plotGeneUsage.R
R/clones.shared.R
R/plotClonesCDR3Length.R
R/plotClonesCopyNumber.R
R/trueDiversity.R
R/plotSequencesMutationBase.R
R/sequences.getOutOfFrames.R
R/readIMGT.R
R/clones.filterSize.R
R/clones.filterFunctionality.R
R/sequences.getProductives.R
R/dist.PCoA.R
R/clones.IDlist.R
R/sequences.getInFrames.R
R/sequences.distance.R
R/plotDistPCoA.R
R/geneUsage.R
R/plotSequencesMutationAA.R
R/sequences.mutation.R
R/sequences.junctionFrame.R
R/compare.trueDiversity.R
R/clones.giniIndex.R
R/sequences.mutation.base.R
R/plotGeneComb.R
R/plotCompareAADistribution.R
R/clones.R
R/compare.geneUsage.R
vignettes
vignettes/vignette.Rmd
MD5
build
build/vignette.rds
DESCRIPTION
man
man/geneUsage.Rd
man/clones.ind.Rd
man/compare.aaDistribution.Rd
man/clones.filterFunctionality.Rd
man/mutationtab.Rd
man/aaseqtab2.Rd
man/clones.shared.Rd
man/compare.trueDiversity.Rd
man/readIMGT.Rd
man/aaseqtab.Rd
man/sequences.junctionFrame.Rd
man/clones.giniIndex.Rd
man/clones.allind.Rd
man/clones.IDlist.Rd
man/clones.Rd
man/sequences.functionality.Rd
man/sequences.distance.Rd
man/sequences.getAnyFunctionality.Rd
man/aaDistribution.Rd
man/sequences.geneComb.Rd
man/dist.PCoA.Rd
man/compare.geneUsage.Rd
man/combineIMGT.Rd
man/plotClonesCopyNumber.Rd
man/sequences.mutation.AA.Rd
man/clones.filterJunctionFrame.Rd
man/ntseqtab.Rd
man/sequences.mutation.Rd
man/sequences.mutation.base.Rd
man/clones.filterSize.Rd
man/summarytab.Rd
man/trueDiversity.Rd
man/geneUsage.distance.Rd
man/clones.CDR3Length.Rd
man/bcRep-package.Rd
man/sequences.getAnyJunctionFrame.Rd
man/vgenes.Rd
bcRep documentation built on May 19, 2017, 4:11 p.m.