To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("LymphoSeq")

In most cases, you don't need to download the package archive at all.

LymphoSeq

 

   

Analyze high-throughput sequencing of T and B cell receptors

Bioconductor version: Release (3.5)

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 and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("LymphoSeq")

Documentation

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

Details

biocViews Alignment, MultipleSequenceAlignment, Sequencing, Software, TargetedResequencing, Technology
Version 1.4.0
In Bioconductor since BioC 3.3 (R-3.3) (1 year)
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
LinkingTo
Suggests knitr, pheatmap, wordcloud, rmarkdown
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Build Report  

Package Archives

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

Package Source LymphoSeq_1.4.0.tar.gz
Windows Binary LymphoSeq_1.4.0.zip
Mac OS X 10.11 (El Capitan) LymphoSeq_1.4.0.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/LymphoSeq/tree/release-3.5
Package Short Url http://bioconductor.org/packages/LymphoSeq/
Package Downloads Report Download Stats

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