recoup

Package: recoup
Type: Package
Title: An R package for the creation of complex genomic profile plots
Author: Panagiotis Moulos <moulos@fleming.gr>
Maintainer: Panagiotis Moulos <moulos@fleming.gr>
Depends: GenomicRanges, GenomicAlignments, ggplot2, ComplexHeatmap
Imports: BiocGenerics, biomaRt, circlize, rtracklayer, plyr
Suggests: grid, GenomeInfoDb, Rsamtools, BiocStyle, knitr, rmarkdown,
zoo, RUnit, BiocInstaller, BSgenome, RSQLite, RMySQL
Enhances: parallel
Description: recoup calculates and plots signal profiles
created from short sequence reads derived from Next
Generation Sequencing technologies. The profiles
provided are either sumarized curve profiles or heatmap
profiles. Currently, recoup supports genomic profile
plots for reads derived from ChIP-Seq and RNA-Seq
experiments. The package uses ggplot2 and ComplexHeatmap
graphics facilities for curve and heatmap coverage
profiles respectively.
License: GPL (>= 3)
Encoding: UTF-8
LazyLoad: yes
LazyData: yes
URL: https://github.com/pmoulos/recoup
biocViews: Software, GeneExpression, Preprocessing, QualityControl,
RNASeq, ChIPSeq, Sequencing, Coverage
VignetteBuilder: knitr
Authors@R: c(person(given="Panagiotis", family="Moulos",
email="moulos@fleming.gr", role=c("aut", "cre")))
Version: 1.0.2
Date: 2016-04-02
Collate: 'annotation.R' 'argcheck.R' 'coverage.R' 'ranges.R' 'recoup.R'
'plot.R' 'profile.R' 'util.R'
NeedsCompilation: no
Packaged: 2016-05-16 06:04:00 UTC; biocbuild

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'recoup' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'recoup'
    finding HTML links ... done
    buildAnnotationStore                    html  
    calcCoverage                            html  
    coverageRef                             html  
    finding level-2 HTML links ... done

    coverageRnaRef                          html  
    getAnnotation                           html  
    getBiotypes                             html  
    kmeansDesign                            html  
    preprocessRanges                        html  
    profileMatrix                           html  
    recoup                                  html  
    recoupCorrelation                       html  
    recoupHeatmap                           html  
    recoupPlot                              html  
    recoupProfile                           html  
    recoup_test_data                        html  
    removeData                              html  
    simpleGetSet                            html  
    sliceObj                                html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (recoup)
Making 'packages.html' ... done