cobindR

Package: cobindR
Title: Finding Co-occuring motifs of transcription factor binding sites
Description: Finding and analysing co-occuring motifs of transcription
factor binding sites in groups of genes
Version: 1.10.0
Date: 2013-07-09
Author: Manuela Benary, Stefan Kroeger, Yuehien Lee, Robert Lehmann
Maintainer: Manuela Benary <manuela.benary@cms.hu-berlin.de>
License: Artistic-2.0
Imports: methods, seqinr, yaml, rtfbs, gplots, mclust, gmp,
BiocGenerics (>= 0.13.8), IRanges, Biostrings, BSgenome,
biomaRt
Suggests: RUnit
Enhances: rGADEM, seqLogo, genoPlotR, parallel, VennDiagram,
RColorBrewer, vcd, MotifDb, snowfall
biocViews: ChIPSeq, CellBiology, MultipleComparison, SequenceMatching
NeedsCompilation: no
Packaged: 2016-05-04 05:01:47 UTC; biocbuild

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'cobindR' ...
** R
** inst
** preparing package for lazy loading
Creating a new generic function for 'sequence' in package 'cobindR'
Creating a generic function for 'write' from package 'base' in package 'cobindR'
Creating a generic function for 'write.fasta' from package 'seqinr' in package 'cobindR'
** help
*** installing help indices
  converting help for package 'cobindR'
    finding HTML links ... done
    SeqObj-class                            html  
    bg_binding_sites                        html  
    finding level-2 HTML links ... done

    bg_pairs                                html  
    bg_sequence_origin                      html  
    bg_sequence_source                      html  
    bg_sequence_type                        html  
    bg_sequences                            html  
    binding_sites                           html  
    cobindRConfiguration                    html  
    cobindr-class                           html  
    cobindr-internal                        html  
    cobindr-package                         html  
    comment                                 html  
    configuration-class                     html  
    configuration                           html  
    downstream                              html  
    experiment_description                  html  
    fdrThreshold                            html  
    find.pairs                              html  
    get.bindingsite.ranges                  html  
    get.pairs                               html  
    get.significant.pairs                   html  
    id                                      html  
    location                                html  
    mart                                    html  
    max_distance                            html  
    name                                    html  
    pValue                                  html  
    pairs                                   html  
    pairs_of_interest                       html  
    path                                    html  
    pfm                                     html  
    pfm_path                                html  
    plot.detrending                         html  
    plot.gc                                 html  
    plot.pairdistance                       html  
    plot.pairdistribution                   html  
    plot.positionprofile                    html  
    plot.positions                          html  
    plot.positions.simple                   html  
    plot.tfbs.heatmap                       html  
    plot.tfbs.venndiagram                   html  
    plot.tfbslogo                           html  
    predicted2pwm                           html  
    pseudocount                             html  
    rtfbs                                   html  
    search.gadem                            html  
    search.pwm                              html  
    seqObj                                  html  
    sequence                                html  
    sequence_origin                         html  
    sequence_source                         html  
    sequence_type                           html  
    sequences                               html  
    species                                 html  
    testCpG                                 html  
    threshold                               html  
    uid                                     html  
    upstream                                html  
    write.bindingsites                      html  
    write.bindingsites.table                html  
    write.pairs                             html  
    write.sequences                         html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (cobindR)
Making 'packages.html' ... done