INSPEcT

Package: INSPEcT
Type: Package
Title: Analysis of 4sU-seq and RNA-seq time-course data
Version: 1.2.2
Date: 2015-12-15
Author: Stefano de Pretis
Maintainer: Stefano de Pretis <ste.depo@gmail.com>
Description: INSPEcT (INference of Synthesis, Processing and
dEgradation rates in Time-Course experiments) analyses 4sU-seq
and RNA-seq time-course data in order to evaluate synthesis,
processing and degradation rates and asses via modeling the
rates that determines changes in mature mRNA levels.
License: GPL-2
Depends: R (>= 3.2), methods, Biobase, BiocParallel
Imports: pROC, deSolve, rootSolve, compiler, preprocessCore,
GenomicFeatures, GenomicRanges, IRanges, BiocGenerics,
GenomicAlignments, Rsamtools, S4Vectors
Suggests: BiocStyle, knitr, TxDb.Mmusculus.UCSC.mm9.knownGene
VignetteBuilder: knitr
biocViews: Sequencing, RNASeq, GeneRegulation, TimeCourse,
SystemsBiology
NeedsCompilation: no
RoxygenNote: 5.0.1
Packaged: 2016-05-16 05:33:11 UTC; biocbuild

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'INSPEcT' ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for 'split' from package 'base' in package 'INSPEcT'
Creating a generic function for 'AIC' from package 'stats' in package 'INSPEcT'
** help
*** installing help indices
  converting help for package 'INSPEcT'
    finding HTML links ... done
    AIC-INSPEcT-method                      html  
    Extract                                 html  
    INSPEcT-class                           html  
    finding level-2 HTML links ... done

    INSPEcT                                 html  
    INSPEcT_diffsteady-class                html  
    INSPEcT_model-class                     html  
    UCSC_mm9_genes_exons                    html  
    UCSC_mm9_genes_introns                  html  
    chisqmodel                              html  
    chisqtest                               html  
    combine                                 html  
    compareSteady                           html  
    dim-INSPEcT-method                      html  
    featureNames-INSPEcT-method             html  
    geneClass                               html  
    getModel                                html  
    inHeatmap                               html  
    labeledSF                               html  
    logLik                                  html  
    makeModelRates                          html  
    makeRPKMs                               html  
    makeSimDataset                          html  
    makeSimModel                            html  
    modelRates                              html  
    modelingParams                          html  
    mycerIds10                              html  
    nGenes                                  html  
    nTpts                                   html  
    newINSPEcT                              html  
    plotGene                                html  
    plotMA                                  html  
    ratePvals                               html  
    ratesFirstGuess                         html  
    ratesFirstGuessVar                      html  
    removeModel                             html  
    rocCurve                                html  
    rocThresholds                           html  
    rpkms                                   html  
    sfPlot                                  html  
    simData1rep                             html  
    simData3rep                             html  
    simRates                                html  
    split                                   html  
    testingParams                           html  
    totalSF                                 html  
    tpts                                    html  
    viewModelRates                          html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (INSPEcT)
Making 'packages.html' ... done