LymphoSeq

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

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4, 3.3

Analyze high-throughput sequencing of T and B cell receptors

Bioconductor version: Development (3.24)

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")):

David Coffey. LymphoSeq: Analyze high-throughput sequencing of T and B cell receptors. doi:10.18129/B9.bioc.LymphoSeq, R package version 1.41.0, https://bioconductor.org/packages/LymphoSeq.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

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

## The following initializes the development version of Bioconductor
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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Alignment, MultipleSequenceAlignment, Sequencing, Software, TargetedResequencing, Technology
Version	1.41.0
In Bioconductor since	BioC 3.3 (R-3.3) (10.5 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
System Requirements
URL

Suggests	knitr, pheatmap, wordcloud, rmarkdown
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	LymphoSeq_1.41.0.tar.gz
Windows Binary (x86_64)	LymphoSeq_1.41.0.zip (64-bit only)
macOS Binary (big-sur-x86_64)	LymphoSeq_1.41.0.tgz
macOS Binary (sonoma-arm64)	LymphoSeq_1.41.0.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