This site is a development preview. As such the content and styling may not be final and is subject to change before going into production. To see more information about the redesign click here.

Menu

Documentation:

R / CRAN packages and documentation

Support

Please read the posting guide. Post questions about Bioconductor to one of the following locations:

LymphoSeq

This is the development version of LymphoSeq; for the stable release version, see LymphoSeq.

Analyze high-throughput sequencing of T and B cell receptors

Bioconductor version: Development (3.18)

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>

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

Installation

To install this package, start R (version "4.3") and enter: 

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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

Details

biocViews Alignment, MultipleSequenceAlignment, Sequencing, Software, TargetedResequencing, Technology
Version 1.29.0
In Bioconductor since BioC 3.3 (R-3.3) (7.5 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
Linking To
Suggests knitr, pheatmap, wordcloud, rmarkdown
System Requirements
Enhances
URL
See More
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 LymphoSeq_1.29.0.tar.gz
Windows Binary LymphoSeq_1.29.0.zip
macOS Binary (x86_64) LymphoSeq_1.29.0.tgz
macOS Binary (arm64) LymphoSeq_1.29.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/LymphoSeq
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/LymphoSeq
Bioc Package Browser https://code.bioconductor.org/browse/LymphoSeq/
Package Short Url https://bioconductor.org/packages/LymphoSeq/
Package Downloads Report Download Stats