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bcRep specifications

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Unique identifier OMICS_13606
Name bcRep
Alternative name B cell receptor repertoire
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 2.0
Computer skills Advanced
Version 1.3.6
Stability Stable
Requirements
stats, gplots, parallel, graphics, utils, grDevices, rmarkdown, knitr, plotrix, foreach, doParallel, pander, ape, vegan, stringdist, proxy, R(≥3.2.2), ineq
Source code URL https://cran.r-project.org/src/contrib/bcRep_1.3.6.tar.gz
Maintained Yes

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  • person_outline Julia Bischof

Publication for B cell receptor repertoire

bcRep citations

 (33)
library_books

Foxp1 controls mature B cell survival and the development of follicular and B 1 B cells

2018
Proc Natl Acad Sci U S A
PMCID: 5866538
PMID: 29507226
DOI: 10.1073/pnas.1711335115

[…] usage of igh or igl (igh and igl v usage exemplarily shown in fig. s3 c and d). these results exclude the possibility that the observed effects in b cell numbers are simply secondary to a skewed b cell receptor repertoire., to study the functional consequences of foxp1 deficiency in b cells, we next measured ig concentrations in sera of unchallenged foxp1flox/del;cd19 mice and controls. […]

library_books

How B Cell Receptor Repertoire Sequencing Can Be Enriched with Structural Antibody Data

2017
Front Immunol
PMCID: 5727015
PMID: 29276518
DOI: 10.3389/fimmu.2017.01753

[…] next-generation sequencing methodologies that can yield millions of immunoglobulin gene sequences in a single sequencing run have already given insights into the steady-state and antigen-stimulated b-cell receptor repertoire (, ). on the other hand, low-throughput techniques such as x-ray crystallography can provide detailed information about individual antibody structures. computational […]

library_books

Immune Repertoire after Immunization As Seen by Next Generation Sequencing and Proteomics

2017
Front Immunol
PMCID: 5650670
PMID: 29085363
DOI: 10.3389/fimmu.2017.01286

[…] of an antigen-specific subset of sequences. one challenge is that not all cells with a rearranged immunoglobulin locus express immunoglobulin protein. distinctions have been found between the b-cell receptor repertoire and the plasma cell repertoire that drives immunoglobulin expression (). another challenge is the tissue niche that is sampled for obtaining sequence information. […]

library_books

Timing of the human prenatal antibody response to Plasmodium falciparum antigens

2017
PLoS One
PMCID: 5614534
PMID: 28950009
DOI: 10.1371/journal.pone.0184571

[…] exposure in utero in developed countries and does not necessarily imply fetuses cannot make germinal centers. total lymphocyte counts increase steadily from 20 wks through 40 wks [] and the b cell receptor repertoire diversifies throughout gestation [,]. thus, the ga at which the fetus is exposed to ag may influence the resulting antibody (ab) response., in the present study, fetal igm […]

library_books

The Complex Interplay between DNA Injury and Repair in Enzymatically Induced Mutagenesis and DNA Damage in B Lymphocytes

2017
Int J Mol Sci
PMCID: 5618525
PMID: 28867784
DOI: 10.3390/ijms18091876

[…] is counteracted by bcl6. consequently, in the absence of bcl6, few small resting pre-b cells survive the transition from large cycling pre-b cell to small resting pre-b cell, leading to a diminished b-cell receptor repertoire, indicating that bcl6 plays a crucial role in the generation of a diverse primary b-cell repertoire [] ()., a large fraction of recurrent chromosomal translocations found […]

library_books

Human Secretory IgM Emerges from Plasma Cells Clonally Related to Gut Memory B Cells and Targets Highly Diverse Commensals

2017
Immunity
PMCID: 5519504
PMID: 28709802
DOI: 10.1016/j.immuni.2017.06.013

[…] the td pathway may become predominant over time due to continuous accumulation of me-a b cells (, )., me-a b cells emerge from gut inductive sites along with pc-as and continuously diversify their b cell receptor repertoire via a microbiota-stimulated adaptation process involving induction of shm and pc-a differentiation in pre-existing gcs ()., in addition to pc-as, the gut mucosa contains […]


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bcRep institution(s)
Institute of Experimental Dermatology, University of Lübeck, Lübeck, Germany
bcRep funding source(s)
Supported by the German science foundations grants: EXC-306 and the GRK1743.

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