Package: LineagePulse
Type: Package
Title: Differential expression analysis and model fitting for
        single-cell RNA-seq data
Version: 1.4.0
Date: 2017-10-09
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'))
Description: LineagePulse is a differential expression and expression model fitting package tailored to single-cell RNA-seq data (scRNA-seq). LineagePulse accounts for batch effects, drop-out and variable sequencing depth. One can use LineagePulse to perform longitudinal differential expression analysis across pseudotime as a continuous coordinate or between discrete groups of cells (e.g. pre-defined clusters or experimental conditions). Expression model fits can be directly extracted from LineagePulse.
License: Artistic-2.0
Encoding: UTF-8
Imports: BiocParallel, circlize, compiler, ComplexHeatmap, ggplot2,
        gplots, grDevices, grid, knitr, Matrix, methods, RColorBrewer,
        SingleCellExperiment, splines, stats, SummarizedExperiment,
        utils
biocViews: ImmunoOncology, Software, StatisticalMethod, TimeCourse,
        Sequencing, DifferentialExpression, GeneExpression,
        CellBiology, CellBasedAssays, SingleCell
Collate: 'srcLineagePulse_classUnions.R' 'main_LineagePulse.R'
        'srcLineagePulse_calcNormConst.R'
        'srcLineagePulse_calcPostDrop.R'
        'srcLineagePulse_classLineagePulseObject.R'
        'srcLineagePulse_decompressParameters.R'
        'srcLineagePulse_evalDropoutModel.R'
        'srcLineagePulse_evalImpulseModel.R'
        'srcLineagePulse_evalLogLik.R'
        'srcLineagePulse_fitMeanDispersion.R'
        'srcLineagePulse_fitDropout.R' 'srcLineagePulse_fitWrapperLP.R'
        'srcLineagePulse_fitModel.R' 'srcLineagePulse_getFits.R'
        'srcLineagePulse_initialiseDispModel.R'
        'srcLineagePulse_initialiseDropModel.R'
        'srcLineagePulse_initialiseImpulseParameters.R'
        'srcLineagePulse_initialiseMuModel.R'
        'srcLineagePulse_plotGene.R' 'srcLineagePulse_processSCData.R'
        'srcLineagePulse_runHypothesisTests.R'
        'srcLineagePulse_simulateDataSet.R'
        'srcLineagePulse_sortGeneTrajectories.R'
RoxygenNote: 6.0.1
VignetteBuilder: knitr
BugReports: https://github.com/YosefLab/LineagePulse/issues
git_url: https://git.bioconductor.org/packages/LineagePulse
git_branch: RELEASE_3_9
git_last_commit: a6e92dd
git_last_commit_date: 2019-05-02
Date/Publication: 2019-05-02
NeedsCompilation: no
Packaged: 2019-05-03 05:04:39 UTC; biocbuild
Author: David S Fischer [aut, cre],
  Fabian Theis [ctb],
  Nir Yosef [ctb]
Maintainer: David S Fischer <david.fischer@helmholtz-muenchen.de>
Built: R 3.6.0; ; 2019-05-03 13:46:15 UTC; windows
