MEDIPS

Package: MEDIPS
Type: Package
Title: DNA IP-seq data analysis
Version: 1.22.0
Date: 2016-04-15
Author: Lukas Chavez, Matthias Lienhard, Joern Dietrich, Isaac Lopez Moyado
Maintainer: Lukas Chavez <l.chavez@dkfz.de>
Description: MEDIPS was developed for analyzing data derived from
methylated DNA immunoprecipitation (MeDIP) experiments followed
by sequencing (MeDIP-seq). However, MEDIPS provides functionalities for the analysis of any kind of quantitative
sequencing data (e.g. ChIP-seq, MBD-seq, CMS-seq and others)
including calculation of differential coverage between groups
of samples and saturation and correlation analysis.
License: GPL (>=2)
LazyLoad: yes
Depends: R (>= 3.0), BSgenome, Rsamtools
Imports: GenomicRanges, Biostrings, graphics, gtools, IRanges, methods,
stats, utils, edgeR, DNAcopy, biomaRt, rtracklayer,
preprocessCore
Suggests: BSgenome.Hsapiens.UCSC.hg19, MEDIPSData, BiocStyle
biocViews: DNAMethylation, CpGIsland, DifferentialExpression,
Sequencing, ChIPSeq, Preprocessing, QualityControl,
Visualization, Microarray, Genetics, Coverage,
GenomeAnnotation, CopyNumberVariation, SequenceMatching
NeedsCompilation: no
Packaged: 2016-05-05 02:41:59 UTC; biocbuild

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'MEDIPS' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'MEDIPS'
    finding HTML links ... done
    COUPLINGset-class                       html  
    MEDIPS-package                          html  
    MEDIPS.CpGenrich                        html  
    MEDIPS.addCNV                           html  
    MEDIPS.correlation                      html  
    MEDIPS.couplingVector                   html  
    MEDIPS.createROIset                     html  
    MEDIPS.createSet                        html  
    MEDIPS.exportWIG                        html  
    MEDIPS.getAnnotation                    html  
    MEDIPS.mergeFrames                      html  
    MEDIPS.mergeSets                        html  
    MEDIPS.meth                             html  
    MEDIPS.plotCalibrationPlot              html  
    MEDIPS.plotSaturation                   html  
    MEDIPS.plotSeqCoverage                  html  
    MEDIPS.saturation                       html  
    MEDIPS.selectROIs                       html  
    MEDIPS.selectSig                        html  
    MEDIPS.seqCoverage                      html  
    MEDIPS.setAnnotation                    html  
    MEDIPSroiSet-class                      html  
    MEDIPSset-class                         html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (MEDIPS)
Making 'packages.html' ... done