bcRep: Advanced Analysis of B Cell Receptor Repertoire Data

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

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

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.