LymphoSeq

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.

Installation instructions

Install release version 1.4

Install from Bioconductor

if (!requireNamespace("BiocManager", quietly=TRUE))
    install.packages("BiocManager")
BiocManager::install("LymphoSeq")

Install developer version 1.5

Option 1: Install from Bioconductor developer branch

# Switch to Bioconductor developer branch (requires latest version of R)
library(BiocManager)
BiocManager::install(version = "devel")

# Download developer release
if (!requireNamespace("BiocManager", quietly=TRUE))
    install.packages("BiocManager")
BiocManager::install("LymphoSeq")

Option 2: Install from GitHub

# Install the latest version of Bioconductor
if (!requireNamespace("BiocManager", quietly=TRUE))
    install.packages("BiocManager")
BiocManager::install()

# Download developer tools
install.packages("devtools")

# Download package from GitHub
devtools::install_github("davidcoffey/LymphoSeqDB")
devtools::install_github("davidcoffey/LymphoSeq")

Documentation

• LymphoSeq vignette
• LymphoSeq manual
• LymphoSeq news

Citation

Coffey D (2017). LymphoSeq: Analyze high-throughput sequencing of T and B cell receptors. R package version 1.4.