r3Cseq

Package: r3Cseq
Version: 1.18.0
Title: Analysis of Chromosome Conformation Capture and Next-generation
Sequencing (3C-seq)
Author: Supat Thongjuea, MRC Molecular Haematology Unit, Weatherall
Institute of Molecular Medicine, University of Oxford, UK
<supat.thongjuea@ndcls.ox.ac.uk>
Maintainer: Supat Thongjuea <supat.thongjuea@ndcls.ox.ac.uk>
Depends: GenomicRanges, Rsamtools, rtracklayer, VGAM, qvalue
Imports: methods, GenomeInfoDb, IRanges, Biostrings, data.table, sqldf,
RColorBrewer
Suggests: BSgenome.Mmusculus.UCSC.mm9.masked,
BSgenome.Mmusculus.UCSC.mm10.masked,
BSgenome.Hsapiens.UCSC.hg18.masked,
BSgenome.Hsapiens.UCSC.hg19.masked,
BSgenome.Rnorvegicus.UCSC.rn5.masked
Description: This package is an implementation of data analysis for the
long-range interactions from 3C-seq assay.
License: GPL-3
URL: http://r3cseq.genereg.net
Collate: AllClasses.R AllGenerics.R Export.R FunctionInCommon.R
FunctionsForBatchAnalysis.R RestrictionEnzymeFunctions.R
FunctionsForNoReplicationAnalysis.R Report.R Visualize3Cseq.R
Annotation.R
biocViews: Preprocessing, Sequencing
NeedsCompilation: no
Packaged: 2016-05-04 04:17:49 UTC; biocbuild

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'r3Cseq' ...
** R
** data
** inst
** preparing package for lazy loading
No methods found in "Biostrings" for requests: DNAString
** help
*** installing help indices
  converting help for package 'r3Cseq'
    finding HTML links ... done
    Myb_prom_FB                             html  
    Myb_prom_FL                             html  
    calculateBatchRPM                       html  
    calculateRPM                            html  
    contrCoverage                           html  
    contrInteractionRegions                 html  
    contrRPM                                html  
    contrRawData                            html  
    contrReadCount                          html  
    enzymeDb                                html  
    expCoverage                             html  
    expInteractionRegions                   html  
    expRPM                                  html  
    expRawData                              html  
    expReadCount                            html  
    export3Cseq2bedGraph                    html  
    export3CseqRawReads2bedGraph            html  
    exportBatchInteractions2text            html  
    exportInteractions2text                 html  
    generate3CseqReport                     html  
    getBatchInteractions                    html  
    finding level-2 HTML links ... done

    getBatchRawReads                        html  
    getBatchReadCountPerRestrictionFragment
                                            html  
    getBatchReadCountPerWindow              html  
    getContrInteractionsInRefseq            html  
    getCoverage                             html  
    getExpInteractionsInRefseq              html  
    getInteractions                         html  
    getRawReads                             html  
    getReadCountPerRestrictionFragment      html  
    getReadCountPerWindow                   html  
    getViewpoint                            html  
    hg18refGene                             html  
    hg19refGene                             html  
    mm10refGene                             html  
    mm9refGene                              html  
    plot3Cecdf                              html  
    plotDomainogramNearViewpoint            html  
    plotInteractionsNearViewpoint           html  
    plotInteractionsPerChromosome           html  
    plotOverviewInteractions                html  
    r3Cseq-class                            html  
    r3CseqCommon-class                      html  
    r3CseqInBatch-class                     html  
    rn5refGene                              html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
No methods found in "Biostrings" for requests: DNAString
* DONE (r3Cseq)
Making 'packages.html' ... done