clonotypeR

This package is for version 3.9 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: 3.9

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 at riken.jp>

Maintainer: Charles Plessy <plessy at riken.jp>

Citation (from within R, enter citation("clonotypeR")):

Installation

To install this package, start R (version "3.6") 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")
clonotypeR User's Guide HTML R Script
Reference Manual PDF
README Text
NEWS Text
LICENSE Text

Details

biocViews Sequencing, Software
Version 1.22.0
In Bioconductor since BioC 2.13 (R-3.0) (10.5 years)
License file LICENSE
Depends
Imports methods
System Requirements
URL http://clonotyper.branchable.com/
Bug Reports http://clonotyper.branchable.com/Bugs/
See More
Suggests BiocGenerics, edgeR, knitr, pvclust, RUnit, vegan
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package clonotypeR_1.22.0.tar.gz
Windows Binary clonotypeR_1.22.0.zip
Mac OS X 10.11 (El Capitan) clonotypeR_1.22.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/clonotypeR
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/clonotypeR
Bioc Package Browser https://code.bioconductor.org/browse/clonotypeR/
Package Short Url https://bioconductor.org/packages/clonotypeR/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.9 Source Archive