LymphoSeq
This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see LymphoSeq.
Analyze high-throughput sequencing of T and B cell receptors
Bioconductor version: 3.9
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("LymphoSeq")):
Installation
To install this package, start R (version "3.6") 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 | ||
| NEWS | Text |
Details
| biocViews | Alignment, MultipleSequenceAlignment, Sequencing, Software, TargetedResequencing, Technology |
| Version | 1.12.0 |
| 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 |
| System Requirements | |
| URL |
See More
| Suggests | knitr, pheatmap, wordcloud, rmarkdown |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | LymphoSeq_1.12.0.tar.gz |
| Windows Binary | LymphoSeq_1.12.0.zip |
| Mac OS X 10.11 (El Capitan) | LymphoSeq_1.12.0.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 |
| Old Source Packages for BioC 3.9 | Source Archive |