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Bioconductor - LymphoSeq (development version)

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 (3.22)

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 "4.5") 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 1.37.0 In Bioconductor since BioC 3.3 (R-3.3) (9 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 See More Package Archives

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

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