Package: ImpulseDE2
Type: Package
Title: Differential expression analysis of longitudinal count data sets
Version: 1.6.1
Date: 2017-04-07
Authors@R: c( person('David S', 'Fischer', NULL,
        'david.fischer@helmholtz-muenchen.de', c('aut','cre')),
        person('Fabian', 'Theis', NULL,
        'fabian.theis@helmholtz-muenchen.de', 'ctb'), person('Nir',
        'Yosef', NULL, 'niryosef@berkeley.edu', 'ctb'))
Author: David S Fischer [aut, cre], Fabian J Theis [ctb], Nir Yosef
        [ctb]
Maintainer: David S Fischer <david.fischer@helmholtz-muenchen.de>
Description: ImpulseDE2 is a differential expression algorithm for
        longitudinal count data sets which arise in sequencing
        experiments such as RNA-seq, ChIP-seq, ATAC-seq and DNaseI-seq.
        ImpulseDE2 is based on a negative binomial noise model with
        dispersion trend smoothing by DESeq2 and uses the impulse model
        to constrain the mean expression trajectory of each gene. The
        impulse model was empirically found to fit global expression
        changes in cells after environmental and developmental stimuli
        and is therefore appropriate in most cell biological scenarios.
        The constraint on the mean expression trajectory prevents
        overfitting to small expression fluctuations. Secondly,
        ImpulseDE2 has higher statistical testing power than
        generalized linear model-based differential expression
        algorithms which fit time as a categorial variable if more than
        six time points are sampled because of the fixed number of
        parameters.
License: Artistic-2.0
Encoding: UTF-8
Imports: Biobase, BiocParallel, ComplexHeatmap, circlize, compiler,
        cowplot, DESeq2, ggplot2, grDevices, knitr, Matrix, methods,
        S4Vectors, stats, SummarizedExperiment, utils
biocViews: ImmunoOncology, Software, StatisticalMethod, TimeCourse,
        Sequencing, DifferentialExpression, GeneExpression,
        CellBiology, CellBasedAssays
Collate: 'ImpulseDE2_main.R' 'srcImpulseDE2_CostFunctionsFit.R'
        'srcImpulseDE2_classImpulseDE2Object.R'
        'srcImpulseDE2_computeNormConst.R'
        'srcImpulseDE2_evalImpulse.R' 'srcImpulseDE2_evalSigmoid.R'
        'srcImpulseDE2_fitImpulse.R' 'srcImpulseDE2_fitSigmoid.R'
        'srcImpulseDE2_plotGenes.R' 'srcImpulseDE2_plotHeatmap.R'
        'srcImpulseDE2_processData.R' 'srcImpulseDE2_runDEAnalysis.R'
        'srcImpulseDE2_runDESeq2.R' 'srcImpulseDE2_simulateDataSet.R'
RoxygenNote: 6.0.1
VignetteBuilder: knitr
BugReports: https://github.com/YosefLab/ImpulseDE2/issues
git_url: https://git.bioconductor.org/packages/ImpulseDE2
git_branch: RELEASE_3_8
git_last_commit: 06b8982
git_last_commit_date: 2019-01-04
Date/Publication: 2019-01-04
NeedsCompilation: no
Packaged: 2019-01-05 04:33:06 UTC; biocbuild
Built: R 3.5.2; ; 2019-01-05 12:16:15 UTC; windows
