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 (3.24)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
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 | ||
| NEWS | Text |
Details
| biocViews | Alignment, MultipleSequenceAlignment, Sequencing, Software, TargetedResequencing, Technology |
| Version | 1.41.0 |
| In Bioconductor since | BioC 3.3 (R-3.3) (10.5 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_1.41.0.tar.gz |
| Windows Binary (x86_64) | LymphoSeq_1.41.0.zip |
| macOS Binary (big-sur-x86_64) | LymphoSeq_1.41.0.tgz |
| macOS Binary (sonoma-arm64) | LymphoSeq_1.41.0.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 |