Rariant

Package: Rariant
Type: Package
Title: Identification and Assessment of Single Nucleotide Variants
through Shifts in Non-Consensus Base Call Frequencies
Version: 1.8.3
Author: Julian Gehring, Simon Anders, Bernd Klaus
Maintainer: Julian Gehring <jg-bioc@gmx.com>
Imports: methods, S4Vectors, IRanges, GenomeInfoDb, ggbio, ggplot2,
exomeCopy, SomaticSignatures, Rsamtools, shiny, VGAM, dplyr,
reshape2
Depends: R (>= 3.0.2), GenomicRanges, VariantAnnotation
Suggests: h5vcData, testthat, knitr, optparse,
BSgenome.Hsapiens.UCSC.hg19
Description: The 'Rariant' package identifies single nucleotide variants from sequencing data based on the difference of binomially distributed mismatch rates between matched samples.
VignetteBuilder: knitr
Encoding: UTF-8
ByteCompile: TRUE
License: GPL-3
URL: https://github.com/juliangehring/Rariant
BugReports: https://support.bioconductor.org
LazyLoad: yes
biocViews: Sequencing, StatisticalMethod, GenomicVariation,
SomaticMutation, VariantDetection, Visualization
NeedsCompilation: no
Packaged: 2016-05-16 04:27:15 UTC; biocbuild

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'Rariant' ...
** R
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import 'ggplot2::Position' by 'BiocGenerics::Position' when loading 'ggbio'
** help
*** installing help indices
  converting help for package 'Rariant'
    finding HTML links ... done
    Rariant-package                         html  
    ci-adjust                               html  
    ci-assessment                           html  
    ci-utils                                html  
    colorscales                             html  
    convert-utils                           html  
    evidence-heatmap                        html  
    mismatch-plot                           html  
    mismatch-utils                          html  
    multi-utils                             html  
    plot-cis                                html  
    prop-cis                                html  
    prop-tests                              html  
    rariant                                 html  
    shiny                                   html  
    split-sample                            html  
    tally                                   html  
    yesnomaybe                              html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import 'ggplot2::Position' by 'BiocGenerics::Position' when loading 'ggbio'
* DONE (Rariant)
Making 'packages.html' ... done