ELMER

Package: ELMER
Title: Inferring Regulatory Element Landscapes and Transcription Factor
Networks Using Cancer Methylomes
Version: 1.4.2
Authors@R: c(person("Lijing", "Yao", role = c("cre", "aut"),
email = "lijingya@usc.edu"),
person("Ben", "Berman", role = "aut"),
person("Peggy", "Farnham", role = "aut"),
person("Hui", "Shen", role = "ctb"),
person("Peter", "Laird", role = "ctb"),
person("Simon","Coetzee", role = "ctb"))
Description:
ELMER is designed to use DNA methylation and gene expression from a large number of samples to infere regulatory element landscape and transcription factor network in primary tissue.
Depends: R (>= 3.2.0), IlluminaHumanMethylation450kanno.ilmn12.hg19,
Homo.sapiens, ELMER.data
License: GPL-3
LazyData: true
VignetteBuilder: knitr
Imports:
methods,BiocGenerics,S4Vectors,IRanges,GenomeInfoDb,GenomicRanges,ggplot2,reshape,grid,gridExtra,minfi,GenomicFeatures
Suggests: parallel, snow, BiocStyle, knitr, R.utils, downloader
biocViews: DNAMethylation, GeneExpression, MotifAnnotation, Software,
GeneRegulation
NeedsCompilation: no
Packaged: 2016-05-16 05:29:23 UTC; biocbuild
Author: Lijing Yao [cre, aut],
Ben Berman [aut],
Peggy Farnham [aut],
Hui Shen [ctb],
Peter Laird [ctb],
Simon Coetzee [ctb]
Maintainer: Lijing Yao <lijingya@usc.edu>

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'ELMER' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'ELMER'
    finding HTML links ... done
    GetNearGenes                            html  
    MEE.data-class                          html  
    Pair-class                              html  
    TCGA.pipe                               html  
    TF.rank.plot                            html  
    fetch.mee                               html  
    fetch.pair                              html  
    get.TFs                                 html  
    get.diff.meth                           html  
    get.enriched.motif                      html  
    finding level-2 HTML links ... done

    get.feature.probe                       html  
    get.pair                                html  
    get.permu                               html  
    get450K                                 html  
    getClinic                               html  
    getExp                                  html  
    getGeneID                               html  
    getGeneInfo                             html  
    getMeth                                 html  
    getPair                                 html  
    getProbeInfo                            html  
    getRNAseq                               html  
    getSample                               html  
    getSymbol                               html  
    getTCGA                                 html  
    motif.enrichment.plot                   html  
    promoterMeth                            html  
    scatter.plot                            html  
    schematic.plot                          html  
    txs                                     html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (ELMER)
Making 'packages.html' ... done