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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
|
This package is for version 3.3 of Bioconductor; for the stable, up-to-date release version, see LymphoSeq.
Analyze high-throughput sequencing of T and B cell receptors
Bioconductor version: 3.3
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
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("LymphoSeq")
| R Script | Analyze high throughput sequencing of T and B cell receptors with LymphoSeq | |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | Sequencing, Software, TargetedResequencing, Technology |
| Version | 1.0.2 |
| In Bioconductor since | BioC 3.3 (R-3.3) (< 6 months) |
| License | Artistic-2.0 |
| Depends | R (>= 3.2), LymphoSeqDB |
| Imports | data.table, plyr, dplyr, reshape, VennDiagram, ggplot2, ineq, RColorBrewer, circlize, grid, utils, stats |
| LinkingTo | |
| Suggests | knitr, pheatmap, wordcloud |
| 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_1.0.2.tar.gz |
| Windows Binary | LymphoSeq_1.0.2.zip |
| Mac OS X 10.9 (Mavericks) | LymphoSeq_1.0.2.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/LymphoSeq/tree/release-3.3 |
| Package Short Url | http://bioconductor.org/packages/LymphoSeq/ |
| Package Downloads Report | Download Stats |
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