clonotypeR

DOI: 10.18129/B9.bioc.clonotypeR    

This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.

This package is for version 3.15 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see clonotypeR.

High throughput analysis of T cell antigen receptor sequences

Bioconductor version: 3.15

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 <charles.plessy at oist.jp>

Maintainer: Charles Plessy <charles.plessy at oist.jp>

Installation

To install this package, start R (version "4.2") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("clonotypeR")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("clonotypeR")

 

HTML	R Script	clonotypeR User's Guide
PDF		Reference Manual
Text		README
Text		NEWS
Text		LICENSE

Details

biocViews	Sequencing, Software
Version	1.34.0
In Bioconductor since	BioC 2.13 (R-3.0) (9 years)
License	file LICENSE
Depends
Imports	methods
LinkingTo
Suggests	BiocGenerics, edgeR, knitr, pvclust, rmarkdown, RUnit, vegan
SystemRequirements
Enhances
URL	http://clonotyper.branchable.com/
BugReports	http://clonotyper.branchable.com/Bugs/
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	clonotypeR_1.34.0.tar.gz
Windows Binary	clonotypeR_1.34.0.zip
macOS Binary (x86_64)	clonotypeR_1.34.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/clonotypeR
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/clonotypeR
Package Short Url	https://bioconductor.org/packages/clonotypeR/
Package Downloads Report	Download Stats