Package: GenoGAM
Type: Package
Title: A GAM based framework for analysis of ChIP-Seq data
Version: 2.4.0
Date: 2019-06-08
Authors@R: c(person("Georg", "Stricker", role = c("aut", "cre"), email
        = "georg.stricker@protonmail.com"), 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
Encoding: UTF-8
Depends: R (>= 3.5), SummarizedExperiment (>= 1.1.19), HDF5Array (>=
        1.8.0), rhdf5 (>= 2.21.6), S4Vectors (>= 0.23.18), Matrix (>=
        1.2-8), data.table (>= 1.9.4)
Imports: Rcpp (>= 0.12.14), sparseinv (>= 0.1.1), Rsamtools (>=
        1.18.2), GenomicRanges (>= 1.23.16), BiocParallel (>= 1.5.17),
        DESeq2 (>= 1.11.23), futile.logger (>= 1.4.1), GenomeInfoDb (>=
        1.7.6), GenomicAlignments (>= 1.7.17), IRanges (>= 2.5.30),
        Biostrings (>= 2.39.14), DelayedArray (>= 0.3.19), methods,
        stats
LinkingTo: Rcpp, RcppArmadillo
Suggests: BiocStyle, chipseq (>= 1.21.2), LSD (>= 3.0.0), genefilter
        (>= 1.54.2), ggplot2 (>= 2.1.0), testthat, knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: yes
RoxygenNote: 6.1.0
biocViews: Regression, DifferentialPeakCalling, ChIPSeq,
        DifferentialExpression, Genetics, Epigenetics, WholeGenome,
        ChipOnChip, ImmunoOncology
Collate: 'Coordinates-class.R' 'GenoGAMFamily-class.R' 'helper.R'
        'GenoGAMSettings-class.R' 'GenoGAM-class.R' 'GenoGAM-package.R'
        'GenoGAMDataSet-class.R' 'GenoGAMDataSetList-class.R'
        'GenoGAMList-class.R' 'GenoGAMSetup-class.R' 'RcppExports.R'
        'background.R' 'broadPeaks.R' 'cv.R' 'diffBinding.R'
        'estimation.R' 'genogam.R' 'hdf5_handler.R' 'misc.R'
        'narrowPeaks.R' 'peakCalling.R' 'plotting.R' 'pvals.R'
        'readData.R' 'sf.R' 'zzz.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@protonmail.com>
git_url: https://git.bioconductor.org/packages/GenoGAM
git_branch: RELEASE_3_10
git_last_commit: 6753a93
git_last_commit_date: 2019-10-29
Date/Publication: 2019-10-29
Packaged: 2019-10-30 01:56:31 UTC; biocbuild
Built: R 3.6.1; x86_64-conda_cos6-linux-gnu; 2019-11-04 17:57:59 UTC; unix
