Package: GenoGAM
Type: Package
Title: A GAM based framework for analysis of ChIP-Seq data
Version: 1.2.1
Date: 2016-10-05
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), Biostrings
        (>= 2.39.14)
Suggests: BiocStyle, chipseq (>= 1.21.2), LSD (>= 3.0.0), genefilter
        (>= 1.54.2), ggplot2 (>= 2.1.0), testthat, knitr
VignetteBuilder: knitr
NeedsCompilation: no
RoxygenNote: 5.0.1
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' 'devel.R' 'diffBinding.R' 'filter.R' 'genogam.R'
        'helper.R' 'peakCalling.R' 'plotting.R' 'qc.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: 2016-10-21 07:26:17 UTC; biocbuild
Built: R 3.3.1; ; 2016-10-21 09:30:38 UTC; windows
