GenoGAM

Package: GenoGAM
Type: Package
Title: A GAM based framework for analysis of ChIP-Seq data
Version: 1.0.2
Date: 2016-03-13
Authors@R: c(person("Georg", "Stricker", role = c("aut", "cre"), email
= "georg.stricker@in.tum.de"), person("Alexander",
"Engelhardt", role = c("aut"), email =
"alexander.engelhardt@ibe.med.uni-muenchen.de"),
person("Julien", "Gagneur", role = c("aut"), email =
"gagneur@in.tum.de") )
Description: This package allows statistical analysis of genome-wide
data with smooth functions using generalized additive models
based on the implementation from the R-package 'mgcv'. It
provides methods for the statistical analysis of ChIP-Seq data
including inference of protein occupancy, and pointwise and
region-wise differential analysis. Estimation of dispersion and
smoothing parameters is performed by cross-validation. Scaling
of generalized additive model fitting to whole chromosomes is
achieved by parallelization over overlapping genomic intervals.
License: GPL-2
LazyData: true
Depends: R (>= 3.3), Rsamtools (>= 1.18.2), SummarizedExperiment (>=
1.1.19), GenomicRanges (>= 1.23.16), methods
Imports: BiocParallel (>= 1.5.17), data.table (>= 1.9.4), DESeq2 (>=
1.11.23), futile.logger (>= 1.4.1), GenomeInfoDb (>= 1.7.6),
GenomicAlignments (>= 1.7.17), IRanges (>= 2.5.30), mgcv (>=
1.8), reshape2 (>= 1.4.1), S4Vectors (>= 0.9.34)
Suggests: BiocStyle, chipseq (>= 1.21.2), testthat, knitr
VignetteBuilder: knitr
NeedsCompilation: no
RoxygenNote: 5.0.1.9000
biocViews: Regression, DifferentialPeakCalling, ChIPSeq,
DifferentialExpression, Genetics, Epigenetics
Collate: 'GenomicTiles-class.R' 'GenoGAMSettings-class.R'
'GenoGAM-class.R' 'GenoGAM-package.R' 'GenoGAMDataSet-class.R'
'cv.R' 'genogam.R' 'helper.R' 'readData.R' 'sf.R'
URL: https://github.com/gstricker/GenoGAM
BugReports: https://github.com/gstricker/GenoGAM/issues
Author: Georg Stricker [aut, cre], Alexander Engelhardt [aut], Julien
Gagneur [aut]
Maintainer: Georg Stricker <georg.stricker@in.tum.de>
Packaged: 2016-05-16 06:04:59 UTC; biocbuild

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'GenoGAM' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'GenoGAM'
    finding HTML links ... done
    GenoGAM-class                           html  
    GenoGAM-view                            html  
    GenoGAM                                 html  
    GenoGAMDataSet-class                    html  
    GenoGAMDataSet                          html  
    GenoGAMDataSetToDataFrame               html  
    GenoGAMSettings-class                   html  
    GenoGAMSettings                         html  
    GenomicTiles-brackets                   html  
    GenomicTiles-class                      html  
Rd warning: /tmp/RtmpW9gy9J/R.INSTALL59a222a2f687/GenoGAM/man/GenomicTiles-class.Rd:21: missing file link 'SummarizedExperiment'
    GenomicTiles-metrics                    html  
    GenomicTiles-view                       html  
    GenomicTiles                            html  
Rd warning: /tmp/RtmpW9gy9J/R.INSTALL59a222a2f687/GenoGAM/man/GenomicTiles.Rd:25: missing file link 'SummarizedExperiment'
    asDataFrame                             html  
    changeSettings                          html  
    checkSettings                           html  
    computeSignificance                     html  
    computeSizeFactors                      html  
    dataRange                               html  
    design                                  html  
    fitGenoGAM                              html  
    getChunkIndex                           html  
    getCoordinates                          html  
    getFits                                 html  
    getIndex                                html  
    getIndexCoordinates                     html  
    getTile                                 html  
    makeTestGenoGAM                         html  
    makeTestGenoGAMDataSet                  html  
    makeTestGenomicTiles                    html  
    sizeFactors                             html  
    subset-GenoGAM-method                   html  
    subset-GenoGAMDataSet-method            html  
    subset-GenomicTiles-method              html  
    subsetByOverlaps-GenoGAM-ANY-method     html  
    subsetByOverlaps-GenoGAMDataSet-GRanges-method
                                            html  
    subsetByOverlaps-GenomicTiles-GRanges-method
                                            html  
    tileSettings-elements                   html  
    tileSettings                            html  
    untile                                  html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (GenoGAM)
Making 'packages.html' ... done