MSstats

Package: MSstats
Title: Protein Significance Analysis in DDA, SRM and DIA for Label-free
or Label-based Proteomics Experiments
Version: 3.4.0
Date: 2016-05-01
Description: A set of tools for statistical relative protein significance analysis in DDA, SRM and DIA experiments.
Author: Meena Choi <mnchoi67@gmail.com>, Lin-Yang Cheng <cheng68@purdue.edu>, Tsung-Heng Tsai <tsai.tsungheng@gmail.com>, Ching-Yun Chang <chang54@purdue.edu>, Olga Vitek <o.vitek@neu.edu>
Maintainer: Meena Choi <mnchoi67@gmail.com>
License: Artistic-2.0
Depends: R (>= 3.2), ggplot2 (>= 2.0.0), Rcpp, grid, reshape2
Imports: lme4, marray, limma, gplots, ggrepel, preprocessCore,
data.table, MSnbase, reshape, survival, minpack.lm
bioViews: Bioinformatics, MassSpectrometry, Proteomics, Software
LazyData: yes
URL: http://msstats.org
BugReports: https://groups.google.com/forum/#!forum/msstats
Packaged: 2016-05-04 05:09:43 UTC; biocbuild
NeedsCompilation: no

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'MSstats' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
Warning: replacing previous import 'reshape::melt' by 'data.table::melt' when loading 'MSstats'
** help
*** installing help indices
  converting help for package 'MSstats'
    finding HTML links ... done
    DDARawData                              html  
    DDARawData.Skyline                      html  
    DIARawData                              html  
    MQtoMSstatsFormat                       html  
    MSstats-package                         html  
    SRMRawData                              html  
    SpikeInDataLinear                       html  
    SpikeInDataNonLinear                    html  
    dataProcess                             html  
    dataProcessPlots                        html  
    designSampleSize                        html  
    designSampleSizePlots                   html  
    groupComparison                         html  
    groupComparisonPlots                    html  
    linear_quantlim                         html  
    modelBasedQCPlots                       html  
    nonlinear_quantlim                      html  
    plot_quantlim                           html  
    quantification                          html  
    transformMSnSetToMSstats                html  
Rd warning: /tmp/Rtmp3soaQV/R.INSTALL797d402880ef/MSstats/man/transformMSnSetToMSstats.Rd:26: missing file link 'MSnSet'
    transformMSstatsToMSnSet                html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import 'reshape::melt' by 'data.table::melt' when loading 'MSstats'
* DONE (MSstats)
Making 'packages.html' ... done