genomation

Package: genomation
Type: Package
Title: Summary, annotation and visualization of genomic data
Version: 1.4.2
Author: Altuna Akalin [aut, cre], Vedran Franke [aut, cre], Katarzyna Wreczycka [aut], Liz Ing-Simmons [ctb]
Maintainer: Altuna Akalin <aakalin@gmail.com>, Vedran Franke <vedran.franke@gmail.com>
Description: A package for summary and annotation of genomic intervals. Users can visualize and
quantify genomic intervals over pre-defined functional regions, such as promoters, exons,
introns, etc. The genomic intervals represent regions with a defined chromosome position,
which may be associated with a score, such as aligned reads from HT-seq experiments, TF binding sites,
methylation scores, etc. The package can use any tabular genomic feature data as long as it has minimal
information on the locations of genomic intervals. In addition, It can use BAM or BigWig files as input.
License: Artistic-2.0
LazyLoad: yes
VignetteBuilder: knitr
biocViews: Annotation, Sequencing, Visualization, CpGIsland
Encoding: latin1
URL: http://bioinformatics.mdc-berlin.de/genomation/
BugReports: https://github.com/BIMSBbioinfo/genomation/issues
Depends: R (>= 3.0.0), grid
Imports: Biostrings, BSgenome, data.table, GenomeInfoDb, GenomicRanges
(>= 1.23.26), GenomicAlignments, S4Vectors (>= 0.9.25),
ggplot2, gridBase, impute, IRanges, matrixStats, methods,
parallel, plotrix, plyr, readr, reshape2, Rsamtools,
seqPattern, rtracklayer,
Suggests: BiocGenerics, genomationData, knitr, knitrBootstrap,
RColorBrewer, rmarkdown, RUnit
Collate: 'documentData.R' 'genomation-classes.R'
'getRandomEnrichment.R' 'findFeatureComb.R' 'patternMatrix.R'
'plotMatrix.R' 'randomizeFeature.R' 'readAnnotate.R'
'readData.R' 'scoreMatrix.R' 'scoreMatrixBin.R'
'scoreMatrixList.R' 'Ops.R' 'test_genomation_package.R'
NeedsCompilation: no
Packaged: 2016-05-16 05:03:47 UTC; biocbuild

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'genomation' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'genomation'
    finding HTML links ... done
    AnnotationByFeature-class               html  
    AnnotationByGeneParts-class             html  
    AnnotationByGeneParts-methods           html  
    Ops-ScoreMatrix-ScoreMatrix-method      html  
    Ops-ScoreMatrixList-ScoreMatrixList-method
                                            html  
    Ops-ScoreMatrixList-numeric-method      html  
    Ops-numeric-ScoreMatrixList-method      html  
    RandomEnrichment-class                  html  
    ScoreMatrix-class                       html  
    ScoreMatrix-methods                     html  
    ScoreMatrixBin-methods                  html  
    ScoreMatrixList-class                   html  
    ScoreMatrixList-methods                 html  
    annotateWithFeature-methods             html  
    annotateWithFeatureFlank-methods        html  
    annotateWithGeneParts-methods           html  
    finding level-2 HTML links ... done

    binMatrix-methods                       html  
    cage                                    html  
    calculateOverlapSignificance-methods    html  
    convertBed2Exons-methods                html  
    convertBed2Introns-methods              html  
    convertBedDf-methods                    html  
    cpgi                                    html  
    findFeatureComb-methods                 html  
    genes                                   html  
    getFeatsWithTargetsStats-methods        html  
    getFlanks-methods                       html  
    getMembers-methods                      html  
    getRandomEnrichment-methods             html  
    getTargetAnnotationStats-methods        html  
    gffToGRanges                            html  
    heatMatrix                              html  
    heatMeta                                html  
    intersectScoreMatrixList-methods        html  
    multiHeatMatrix                         html  
    orderBy-methods                         html  
    patternMatrix-methods                   html  
    plotGeneAnnotation-methods              html  
    plotMeta                                html  
    plotTargetAnnotation-methods            html  
    promoters                               html  
    randomizeFeature-methods                html  
    readBed                                 html  
    readBroadPeak                           html  
    readFeatureFlank-methods                html  
    readGeneric                             html  
    readNarrowPeak                          html  
    readTranscriptFeatures-methods          html  
    scaleScoreMatrix-methods                html  
    scaleScoreMatrixList                    html  
    show-methods                            html  
    sub-ScoreMatrix-ANY-ANY-method          html  
    sub-ScoreMatrixList-ANY-ANY-method      html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (genomation)
Making 'packages.html' ... done