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("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 | ||
| 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 [email protected]: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 |