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LymphoSeq

Analyze high-throughput sequencing of T and B cell receptors


Bioconductor version: Release (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")

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 1.30.0
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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Suggests knitr, pheatmap, wordcloud, rmarkdown
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Package Archives

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

Source Package LymphoSeq_1.30.0.tar.gz
Windows Binary LymphoSeq_1.30.0.zip
macOS Binary (x86_64) LymphoSeq_1.30.0.tgz
macOS Binary (arm64) LymphoSeq_1.30.0.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