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.

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

Files in this package

bcRep
bcRep/inst
bcRep/inst/NEWS.pdf
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/clones.IDlist.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.IDlist.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

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

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