clonotypeR: High throughput analysis of T cell antigen receptor sequences
Version 1.14.0

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.

AuthorCharles Plessy <plessy@riken.jp>
Bioconductor views Sequencing
Date of publicationNone
MaintainerCharles Plessy <plessy@riken.jp>
Licensefile LICENSE
Version1.14.0
URL http://clonotyper.branchable.com/
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("clonotypeR")

Popular 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
unique_clonotypes: unique_clonotypes
yassai_identifier: yassai_identifier
See all...

All man pages Function index File listing

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

Functions

J_before_FGxG Man page
V_after_C Man page
clonotypeR Man page
clonotypeR-package Man page
clonotype_table Man page Source code
codon_ids Man page
common_clonotypes Man page
common_clonotypes,character,character,missing,data.frame-method Man page
common_clonotypes,character,missing,missing,data.frame-method Man page
common_clonotypes,missing,missing,ANY,data.frame-method Man page
common_clonotypes,missing,missing,ANY,matrix-method Man page
is_unproductive Man page Source code
private_clonotypes Man page Source code
read_clonotypes Man page Source code
unique_clonotypes Man page Source code
yassai_identifier Man page
yassai_identifier,ANY,missing,missing,ANY-method Man page
yassai_identifier,character,data.frame,data.frame,ANY-method Man page
yassai_identifier,data.frame,data.frame,data.frame,logical-metho Man page

Files

ChangeLog
DESCRIPTION
LICENSE
NAMESPACE
NEWS
R
R/clonotypeR.R
R/clonotype_table.R
R/common_clonotypes.R
R/is_unproductive.R
R/private_clonotypes.R
R/read_clonotypes.R
R/unique_clonotypes.R
R/yassai_identifier.R
README
build
build/vignette.rds
inst
inst/CITATION
inst/doc
inst/doc/clonotypeR.R
inst/doc/clonotypeR.Rmd
inst/doc/clonotypeR.html
inst/extdata
inst/extdata/J_before_FGxG.txt.gz
inst/extdata/V_after_C.txt.gz
inst/extdata/clonotypes.txt.gz
inst/extdata/clonotypes2.tsv.xz
inst/extdata/codon_ids.txt.gz
inst/unitTests
inst/unitTests/test_yassai_identifier.R
man
man/clonotypeR.Rd
man/clonotype_table.Rd
man/clonotyper_extdata.Rd
man/common_clonotypes.Rd
man/is_unproductive.Rd
man/private_clonotypes.Rd
man/read_clonotypes.Rd
man/unique_clonotypes.Rd
man/yassai_identifier.Rd
tests
tests/runTests.R
vignettes
vignettes/clonotypeR.Rmd
clonotypeR documentation built on May 20, 2017, 9:34 p.m.

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