TCC

Package: TCC
Type: Package
Title: TCC: Differential expression analysis for tag count data with
robust normalization strategies
Version: 1.12.1
Author: Jianqiang Sun, Tomoaki Nishiyama, Kentaro Shimizu, and Koji
Kadota
Maintainer: Jianqiang Sun <wukong@bi.a.u-tokyo.ac.jp>, Tomoaki
Nishiyama <tomoakin@staff.kanazawa-u.ac.jp>
Description: This package provides a series of functions for performing
differential expression analysis from RNA-seq count data using
robust normalization strategy (called DEGES). The basic idea of
DEGES is that potential differentially expressed genes or
transcripts (DEGs) among compared samples should be removed
before data normalization to obtain a well-ranked gene list
where true DEGs are top-ranked and non-DEGs are bottom ranked.
This can be done by performing a multi-step normalization
strategy (called DEGES for DEG elimination strategy). A major
characteristic of TCC is to provide the robust normalization
methods for several kinds of count data (two-group with or
without replicates, multi-group/multi-factor, and so on) by
virtue of the use of combinations of functions in depended
packages.
Depends: R (>= 2.15), methods, DESeq, DESeq2, edgeR, baySeq, ROC
Imports: samr
Suggests: RUnit, BiocGenerics
Enhances: snow
License: GPL-2
Copyright: Authors listed above
biocViews: Sequencing, DifferentialExpression, RNASeq
NeedsCompilation: no
Packaged: 2016-05-27 04:20:14 UTC; biocbuild

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'TCC' ...
** R
** data
** inst
** preparing package for lazy loading
Creating a new generic function for 'calcNormFactors' in package 'TCC'
** help
*** installing help indices
  converting help for package 'TCC'
    finding HTML links ... done
    ROKU                                    html  
    TCC-class                               html  
    TCC                                     html  
    WAD                                     html  
    arab                                    html  
    calcAUCValue                            html  
    calcNormFactors                         html  
    clusterSample                           html  
    estimateDE                              html  
Rd warning: /tmp/Rtmpwz2z7J/R.INSTALL74cd413f7475/TCC/man/estimateDE.Rd:57: missing file link 'glmFit'
Rd warning: /tmp/Rtmpwz2z7J/R.INSTALL74cd413f7475/TCC/man/estimateDE.Rd:66: missing file link 'glmLRT'
Rd warning: /tmp/Rtmpwz2z7J/R.INSTALL74cd413f7475/TCC/man/estimateDE.Rd:73: missing file link 'glmLRT'
Rd warning: /tmp/Rtmpwz2z7J/R.INSTALL74cd413f7475/TCC/man/estimateDE.Rd:81: missing file link 'getPriors.NB'
Rd warning: /tmp/Rtmpwz2z7J/R.INSTALL74cd413f7475/TCC/man/estimateDE.Rd:129: missing file link 'glmFit'
Rd warning: /tmp/Rtmpwz2z7J/R.INSTALL74cd413f7475/TCC/man/estimateDE.Rd:130: missing file link 'glmLRT'
Rd warning: /tmp/Rtmpwz2z7J/R.INSTALL74cd413f7475/TCC/man/estimateDE.Rd:154: missing file link 'getPriors.NB'
Rd warning: /tmp/Rtmpwz2z7J/R.INSTALL74cd413f7475/TCC/man/estimateDE.Rd:168: missing file link 'eBayes'
    filterLowCountGenes                     html  
    getNormalizedData                       html  
    getResult                               html  
Rd warning: /tmp/Rtmpwz2z7J/R.INSTALL74cd413f7475/TCC/man/getResult.Rd:20: missing file link 'plot'
    hypoData                                html  
    hypoData_mg                             html  
    hypoData_ts                             html  
    makeFCMatrix                            html  
    nakai                                   html  
    plot.TCC                                html  
    plotFCPseudocolor                       html  
    simulateReadCounts                      html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (TCC)
Making 'packages.html' ... done