LymphoSeq

Package: LymphoSeq
Title: Analyze high-throughput sequencing of T and B cell receptors
Version: 1.0.2
Author: David Coffey <dcoffey@fredhutch.org>
Maintainer: David Coffey <dcoffey@fredhutch.org>
Description: 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.
Depends: R (>= 3.2), LymphoSeqDB
Imports: data.table, plyr, dplyr, reshape, VennDiagram, ggplot2, ineq,
RColorBrewer, circlize, grid, utils, stats
License: Artistic-2.0
LazyData: true
RoxygenNote: 5.0.1
Suggests: knitr, pheatmap, wordcloud
VignetteBuilder: knitr
biocViews: Software, Technology, Sequencing, TargetedResequencing
NeedsCompilation: no
Packaged: 2016-05-16 06:10:55 UTC; biocbuild

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'LymphoSeq' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'LymphoSeq'
    finding HTML links ... done
    bhattacharyyaCoefficient                html  
    bhattacharyyaMatrix                     html  
    chordDiagramVDJ                         html  
    clonality                               html  
    cloneTrack                              html  
    commonSeqs                              html  
    commonSeqsPlot                          html  
    commonSeqsVenn                          html  
    geneFreq                                html  
    lorenzCurve                             html  
    mergeFiles                              html  
    pairwisePlot                            html  
    productive                              html  
    productiveSeq                           html  
    readImmunoSeq                           html  
    removeSeq                               html  
    searchPublished                         html  
    searchSeq                               html  
    seqMatrix                               html  
    similarityMatrix                        html  
    similarityScore                         html  
    topFreq                                 html  
    topSeqs                                 html  
    topSeqsPlot                             html  
    uniqueSeqs                              html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (LymphoSeq)
Making 'packages.html' ... done