LymphoSeq

This package is for version 3.6 of Bioconductor; for the stable, up-to-date release version, see LymphoSeq.

Analyze high-throughput sequencing of T and B cell receptors


Bioconductor version: 3.6

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 "3.4") and enter:


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

BiocManager::install("LymphoSeq")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

Reference Manual PDF
NEWS Text

Details

biocViews Alignment, MultipleSequenceAlignment, Sequencing, Software, TargetedResequencing, Technology
Version 1.6.0
In Bioconductor since BioC 3.3 (R-3.3) (8 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
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Package Archives

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

Source Package LymphoSeq_1.6.0.tar.gz
Windows Binary LymphoSeq_1.6.0.zip
Mac OS X 10.11 (El Capitan) LymphoSeq_1.6.0.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/
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Old Source Packages for BioC 3.6 Source Archive