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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
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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 |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | Alignment, MultipleSequenceAlignment, Sequencing, Software, TargetedResequencing, Technology |
| Version | 1.4.1 |
| In Bioconductor since | BioC 3.3 (R-3.3) (1.5 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 |
| 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.
| Source Package | LymphoSeq_1.4.1.tar.gz |
| Windows Binary | LymphoSeq_1.4.1.zip |
| Mac OS X 10.11 (El Capitan) | LymphoSeq_1.4.1.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/LymphoSeq |
| Package Short Url | http://bioconductor.org/packages/LymphoSeq/ |
| Package Downloads Report | Download Stats |
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