clonotypeR: High throughput analysis of T cell antigen receptor sequences

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High throughput analysis of T cell antigen receptor sequences The genes encoding T cell receptors are created by somatic recombination, generating an immense combination of V, (D) and J segments. Additional processes during the recombination create extra sequence diversity between the V an J segments. Collectively, this hyper-variable region is called the CDR3 loop. The purpose of this package is to process and quantitatively analyse millions of V-CDR3-J combination, called clonotypes, from multiple sequence libraries.

Author
Charles Plessy <plessy@riken.jp>
Date of publication
None
Maintainer
Charles Plessy <plessy@riken.jp>
License
file LICENSE
Version
1.12.0
URLs

View on Bioconductor

Man pages

clonotypeR
clonotypeR: High throughput analysis of T cell antigen...
clonotyper_extdata
Extra data used to calculate ID numbers in Yassai et al.'s...
clonotype_table
clonotype_table
common_clonotypes
common_clonotypes
is_unproductive
is_unproductive
private_clonotypes
private_clonotypes
read_clonotypes
read_clonotypes
unique_clonotypes
unique_clonotypes
yassai_identifier
yassai_identifier

Files in this package

clonotypeR/ChangeLog
clonotypeR/DESCRIPTION
clonotypeR/LICENSE
clonotypeR/NAMESPACE
clonotypeR/NEWS
clonotypeR/R
clonotypeR/R/clonotypeR.R
clonotypeR/R/clonotype_table.R
clonotypeR/R/common_clonotypes.R
clonotypeR/R/is_unproductive.R
clonotypeR/R/private_clonotypes.R
clonotypeR/R/read_clonotypes.R
clonotypeR/R/unique_clonotypes.R
clonotypeR/R/yassai_identifier.R
clonotypeR/README
clonotypeR/build
clonotypeR/build/vignette.rds
clonotypeR/inst
clonotypeR/inst/CITATION
clonotypeR/inst/doc
clonotypeR/inst/doc/clonotypeR.R
clonotypeR/inst/doc/clonotypeR.Rmd
clonotypeR/inst/doc/clonotypeR.html
clonotypeR/inst/extdata
clonotypeR/inst/extdata/J_before_FGxG.txt.gz
clonotypeR/inst/extdata/V_after_C.txt.gz
clonotypeR/inst/extdata/clonotypes.txt.gz
clonotypeR/inst/extdata/clonotypes2.tsv.xz
clonotypeR/inst/extdata/codon_ids.txt.gz
clonotypeR/inst/unitTests
clonotypeR/inst/unitTests/test_yassai_identifier.R
clonotypeR/man
clonotypeR/man/clonotypeR.Rd
clonotypeR/man/clonotype_table.Rd
clonotypeR/man/clonotyper_extdata.Rd
clonotypeR/man/common_clonotypes.Rd
clonotypeR/man/is_unproductive.Rd
clonotypeR/man/private_clonotypes.Rd
clonotypeR/man/read_clonotypes.Rd
clonotypeR/man/unique_clonotypes.Rd
clonotypeR/man/yassai_identifier.Rd
clonotypeR/tests
clonotypeR/tests/runTests.R
clonotypeR/vignettes
clonotypeR/vignettes/clonotypeR.Rmd