BCellMA: B Cell Receptor Somatic Hyper Mutation Analysis

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Includes a set of functions to analyze for instance nucleotide frequencies as well as transition and transversion. Can reconstruct germline sequences based on the international ImMunoGeneTics information system (IMGT/HighV-QUEST) outputs, calculate and plot the difference (%) of nucleotides at 6 positions around a mutation to identify and characterize hotspot motifs as well as calculate and plot average mutation frequencies of nucleotide mutations resulting in amino acid substitution.

Author
Olena Ohlei <olena.ohlei@student.uni-luebeck.de>
Date of publication
2016-11-29 18:10:28
Maintainer
Olena Ohlei <olena.ohlei@student.uni-luebeck.de>
License
GPL (>= 2)
Version
0.3.2
URLs

View on CRAN

Man pages

aa_cdr3_dist
Average frequency of nucleotide mutations resulting in amino...
aa_dist
Average frequency of nucleotide mutations resulting in amino...
aa_plot
Plot of average frequency of nucleotide mutations resulting...
germlineReconstr
Function to reconstruction of germline sequencies based on...
IMGTtab2
IMGT Table 2
IMGTtab7
IMGT Table 7
IMGTtab8
IMGT Table 8
Klassen
Klassen
na_funktion
The function to check for reconsrtruction errors
nucleotide_mutation
The frequencies of nucleotide mutations and the frequencies...
targetingMatrix
Function to the calculation of the number of Nucleotids at...
targeting_motiv
Function to calculate the difference at three positions...
targeting_motive_plot
Polt of the difference at three positions before and after a...

Files in this package

BCellMA
BCellMA/inst
BCellMA/inst/doc
BCellMA/inst/doc/vignette.Rmd
BCellMA/inst/doc/vignette.R
BCellMA/inst/doc/vignette.html
BCellMA/NAMESPACE
BCellMA/data
BCellMA/data/IMGTtab2.rda
BCellMA/data/IMGTtab8.rda
BCellMA/data/IMGTtab7.rda
BCellMA/data/Klassen.rda
BCellMA/data/datalist
BCellMA/R
BCellMA/R/aa_plot.R
BCellMA/R/targeting_motive_plot.R
BCellMA/R/targeting_motiv.R
BCellMA/R/na_funktion.R
BCellMA/R/targetingMatrix.R
BCellMA/R/data.R
BCellMA/R/aa_cdr3_dist.R
BCellMA/R/aa_zaehlen2.R
BCellMA/R/intern.R
BCellMA/R/aa_zaehlen2_CDR3.R
BCellMA/R/nucleotide_matation.R
BCellMA/R/germlineReconstr.R
BCellMA/R/aa_dist.R
BCellMA/R/lettersPlot_minus.R
BCellMA/vignettes
BCellMA/vignettes/vignette.Rmd
BCellMA/MD5
BCellMA/build
BCellMA/build/vignette.rds
BCellMA/DESCRIPTION
BCellMA/man
BCellMA/man/aa_dist.Rd
BCellMA/man/na_funktion.Rd
BCellMA/man/aa_plot.Rd
BCellMA/man/targeting_motive_plot.Rd
BCellMA/man/IMGTtab8.Rd
BCellMA/man/IMGTtab2.Rd
BCellMA/man/IMGTtab7.Rd
BCellMA/man/targeting_motiv.Rd
BCellMA/man/nucleotide_mutation.Rd
BCellMA/man/aa_cdr3_dist.Rd
BCellMA/man/germlineReconstr.Rd
BCellMA/man/targetingMatrix.Rd
BCellMA/man/Klassen.Rd