segmentSeq

Package: segmentSeq
Type: Package
Title: Methods for identifying small RNA loci from high-throughput
sequencing data
Version: 2.6.0
Date: 2010-01-20
Author: Thomas J. Hardcastle
Maintainer: Thomas J. Hardcastle <tjh48@cam.ac.uk>
Description: High-throughput sequencing technologies allow the production of large volumes of short sequences, which can be aligned to the genome to create a set of matches to the genome. By looking for regions of the genome which to which there are high densities of matches, we can infer a segmentation of the genome into regions of biological significance. The methods in this package allow the simultaneous segmentation of data from multiple samples, taking into account replicate data, in order to create a consensus segmentation. This has obvious applications in a number of classes of sequencing experiments, particularly in the discovery of small RNA loci and novel mRNA transcriptome discovery.
License: GPL-3
LazyLoad: yes
Depends: R (>= 2.3.0), methods, baySeq (>= 1.99.0), ShortRead,
GenomicRanges, IRanges, S4Vectors
Suggests: BiocStyle, BiocGenerics
Imports: graphics, grDevices, utils
biocViews: MultipleComparison, Sequencing, Alignment,
DifferentialExpression, QualityControl, DataImport
Packaged: 2016-05-04 04:02:57 UTC; biocbuild
NeedsCompilation: no

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'segmentSeq' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'segmentSeq'
    finding HTML links ... done
    SL                                      html  
    alignmentClass-class                    html  
    alignmentData-class                     html  
    alignmentMeth-class                     html  
    averageMethylationRegions               html  
    finding level-2 HTML links ... done

    classifySeg                             html  
Rd warning: /tmp/Rtmp5o9xut/R.INSTALL327a67835baa/segmentSeq/man/classifySeg.Rd:44: missing file link 'getPriors.NB'
    findChunks                              html  
    getCounts                               html  
    getOverlaps                             html  
    heuristicSeg                            html  
    lociData-class                          html  
    lociLikelihoods                         html  
Rd warning: /tmp/Rtmp5o9xut/R.INSTALL327a67835baa/segmentSeq/man/lociLikelihoods.Rd:26: missing file link 'getLikelihoods.NB'
    mergeMethSegs                           html  
    methData-class                          html  
    plotGenome                              html  
    plotMeth                                html  
    plotMethDistribution                    html  
    processAD                               html  
    readMethods                             html  
    readMeths                               html  
    segClass-class                          html  
Rd warning: /tmp/Rtmp5o9xut/R.INSTALL327a67835baa/segmentSeq/man/segClass-class.Rd:22: missing file link 'GRanges'
    segData-class                           html  
Rd warning: /tmp/Rtmp5o9xut/R.INSTALL327a67835baa/segmentSeq/man/segData-class.Rd:24: missing file link 'GRanges'
    segMeth-class                           html  
Rd warning: /tmp/Rtmp5o9xut/R.INSTALL327a67835baa/segmentSeq/man/segMeth-class.Rd:24: missing file link 'GRanges'
    segmentSeq-package                      html  
    selectLoci                              html  
    summariseLoci                           html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (segmentSeq)
Making 'packages.html' ... done