Package: tradeSeq
Type: Package
Title: trajectory-based differential expression analysis for sequencing
        data
Date: 2019-03-15
Version: 1.0.0
Authors@R: c(person("Koen", "Van den Berge", role = c("aut"),
                     email = "koen.vandenberge@ugent.be"),
              person("Hector", "Roux de Bezieux", role = c("aut", "cre"),
                     email = "hector.rouxdebezieux@berkeley.edu",
		     comment = c(ORCID = "0000-0002-1489-8339")),
		person("Kelly","Street", role = "ctb"),
		person("Lieven","Clement", role="ctb"),
		person("Sandrine","Dudoit", role="ctb"))
Description: tradeSeq provides a flexible method for finding genes that are differentially expressed along one or multiple trajectories, using a variety of tests suited to answer questions of interest, e.g. the discovery of genes that whose expression is associated with pseudotime, or who are differentially expressed (in a specific region) along the trajectory. It fits a generalized additive model (GAM) for each gene, and performs inference on the parameters of the GAM.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: false
URL: https://statomics.github.io/tradeSeq/index.html
Depends: R (>= 3.6)
Collate: 'AllGenerics.R' 'utils.R' 'associationTest.R'
        'clusterExpressionPatterns.R' 'data.R' 'diffEndTest.R'
        'earlyDETest.R' 'evaluateK.R' 'fitGAM.R' 'getSmootherPvalues.R'
        'getSmootherTestStats.R' 'patternTest.R' 'plotGeneCount.R'
        'plotSmoothers.R' 'startVsEndTest.R'
RoxygenNote: 6.1.1
Imports: mgcv, edgeR, SingleCellExperiment, SummarizedExperiment,
        slingshot, magrittr, RColorBrewer, clusterExperiment,
        BiocParallel, pbapply, ggplot2, princurve, methods, S4Vectors
Suggests: knitr, rmarkdown, cowplot, dplyr, tidyr, testthat
VignetteBuilder: knitr
biocViews: Clustering, Regression, TimeCourse, DifferentialExpression,
        GeneExpression, RNASeq, Sequencing, Software, SingleCell,
        Transcriptomics, MultipleComparison, Visualization
BugReports: https://github.com/statOmics/tradeSeq/issues
git_url: https://git.bioconductor.org/packages/tradeSeq
git_branch: RELEASE_3_10
git_last_commit: b120796
git_last_commit_date: 2019-10-29
Date/Publication: 2019-10-29
NeedsCompilation: no
Packaged: 2019-10-30 04:10:26 UTC; biocbuild
Author: Koen Van den Berge [aut],
  Hector Roux de Bezieux [aut, cre]
    (<https://orcid.org/0000-0002-1489-8339>),
  Kelly Street [ctb],
  Lieven Clement [ctb],
  Sandrine Dudoit [ctb]
Maintainer: Hector Roux de Bezieux <hector.rouxdebezieux@berkeley.edu>
Built: R 3.6.1; ; 2019-11-03 17:20:01 UTC; unix
