CAGEr

Package: CAGEr
Title: Analysis of CAGE (Cap Analysis of Gene Expression) sequencing
data for precise mapping of transcription start sites and
promoterome mining
Version: 1.14.0
Date: 04-27-2016
Author: Vanja Haberle, Department of Biology, University of Bergen, Norway <vanja.haberle@gmail.com>
Maintainer: Vanja Haberle <vanja.haberle@gmail.com>
Imports: utils, Rsamtools, GenomicRanges (>= 1.23.16), IRanges (>=
2.5.27), data.table, beanplot, rtracklayer, som, VGAM
Depends: methods, R (>= 2.15.0), BSgenome
Suggests: BSgenome.Drerio.UCSC.danRer7, FANTOM3and4CAGE
Enhances: parallel
Description: Preprocessing of CAGE sequencing data, identification and normalization of transcription start sites and downstream analysis of transcription start sites clusters (promoters).
License: GPL-3
biocViews: Preprocessing, Sequencing, Normalization,
FunctionalGenomics, Transcription, GeneExpression, Clustering,
Visualization
Collate: AllClasses.R GetMethods.R ImportFunctions.R ImportMethods.R
CorrelationMethods.R ExportFunctions.R ExportMethods.R
MergingMethods.R NormalizationFunctions.R
NormalizationMethods.R ExpressionProfilingMethods.R
ClusteringFunctions.R ClusteringMethods.R
CumulativeDistributionFunctions.R
CumulativeDistributionMethods.R QuantileWidthFunctions.R
QuantileWidthMethods.R AggregationFunctions.R
AggregationMethods.R ShiftingFunctions.R ShiftingMethods.R
NeedsCompilation: no
Packaged: 2016-05-04 04:53:16 UTC; biocbuild

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'CAGEr' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'CAGEr'
    finding HTML links ... done
    CAGEr-package                           html  
    CAGEset-class                           html  
    CTSSclusteringMethod                    html  
    CTSScoordinates                         html  
    CTSSnormalizedTpm                       html  
    CTSStagCount                            html  
    FANTOM5humanSamples                     html  
    FANTOM5mouseSamples                     html  
    aggregateTagClusters                    html  
    clusterCTSS                             html  
    consensusClusters                       html  
    consensusClustersTpm                    html  
    cumulativeCTSSdistribution              html  
    exampleCAGEset                          html  
    exportCTSStoBedGraph                    html  
    exportToBed                             html  
    expressionClasses                       html  
    extractExpressionClass                  html  
    genomeName                              html  
    getCTSS                                 html  
    getExpressionProfiles                   html  
    getShiftingPromoters                    html  
    importPublicData                        html  
    inputFiles                              html  
    inputFilesType                          html  
    librarySizes                            html  
    mergeCAGEsets                           html  
    mergeSamples                            html  
    normalizeTagCount                       html  
    plotCorrelation                         html  
    plotExpressionProfiles                  html  
    plotInterquantileWidth                  html  
    plotReverseCumulatives                  html  
    quantilePositions                       html  
    sampleLabels                            html  
    scoreShift                              html  
    setColors                               html  
    show-methods                            html  
    tagClusters                             html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (CAGEr)
Making 'packages.html' ... done