LymphoSeq

DOI: 10.18129/B9.bioc.LymphoSeq    

This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see LymphoSeq.

Analyze high-throughput sequencing of T and B cell receptors

Bioconductor version: 3.11

This R package analyzes high-throughput sequencing of T and B cell receptor complementarity determining region 3 (CDR3) sequences generated by Adaptive Biotechnologies' ImmunoSEQ assay. Its input comes from tab-separated value (.tsv) files exported from the ImmunoSEQ analyzer.

Author: David Coffey <dcoffey at fredhutch.org>

Maintainer: David Coffey <dcoffey at fredhutch.org>

Installation

To install this package, start R (version "4.0") and enter:

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

BiocManager::install("LymphoSeq")

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("LymphoSeq")

 

HTML	R Script	Analysis of high-throughput sequencing of T and B cell receptors with LymphoSeq
PDF		Reference Manual
Text		NEWS

Details

biocViews	Alignment, MultipleSequenceAlignment, Sequencing, Software, TargetedResequencing, Technology
Version	1.16.0
In Bioconductor since	BioC 3.3 (R-3.3) (4.5 years)
License	Artistic-2.0
Depends	R (>= 3.3), LymphoSeqDB
Imports	data.table, plyr, dplyr, reshape, VennDiagram, ggplot2, ineq, RColorBrewer, circlize, grid, utils, stats, ggtree, msa, Biostrings, phangorn, stringdist, UpSetR
LinkingTo
Suggests	knitr, pheatmap, wordcloud, rmarkdown
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
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Build Report

Package Archives

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

Source Package	LymphoSeq_1.16.0.tar.gz
Windows Binary	LymphoSeq_1.16.0.zip
macOS 10.13 (High Sierra)	LymphoSeq_1.16.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/LymphoSeq
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/LymphoSeq
Package Short Url	https://bioconductor.org/packages/LymphoSeq/
Package Downloads Report	Download Stats