Package: dearseq
Type: Package
Title: Differential Expression Analysis for RNA-seq data through a
        robust variance component test
Version: 1.0.0
Date: 2020-04-04
Authors@R: c(person("Denis", "Agniel", role = c("aut"),
                    email = "denis.agniel@gmail.com"),
	           person("Boris P.", "Hejblum", role = c("aut", "cre"),
	                  email = "boris.hejblum@u-bordeaux.fr"),
	           person("Marine", "Gauthier", role = c("aut"),
	                  email = "marine.gauthier@u-bordeaux.fr"))
Depends: R (>= 3.6.0)
Imports: CompQuadForm, ggplot2, KernSmooth, matrixStats, methods,
        parallel, pbapply, stats, statmod
Suggests: Biobase, BiocManager, BiocSet, edgeR, DESeq2, GEOquery, GSA,
        knitr, limma, readxl, rmarkdown, S4Vectors,
        SummarizedExperiment, testthat, covr
Description: Differential Expression Analysis RNA-seq data with variance 
             component score test accounting for data heteroscedasticity through
             precision weights. Perform both gene-wise and gene set analyses, 
             and can deal with repeated or longitudinal data. Methods are 
             detailed in: Agniel D & Hejblum BP (2017) Variance component score 
             test for time-course gene set analysis of longitudinal RNA-seq 
             data, Biostatistics, 18(4):589-604. and Gauthier M, Agniel D, 
             Thiébaut R & Hejblum BP (2019). dearseq: a variance component 
             score test for RNA-Seq differential analysis that effectively 
             controls the false discovery rate, *bioRxiv* 635714.
LazyData: true
License: GPL-2 | file LICENSE
biocViews: BiomedicalInformatics, CellBiology, DifferentialExpression,
        DNASeq, GeneExpression, Genetics, GeneSetEnrichment,
        ImmunoOncology, KEGG, Regression, RNASeq, Sequencing,
        SystemsBiology, TimeCourse, Transcription, Transcriptomics
BugReports: https://github.com/borishejblum/dearseq/issues
Encoding: UTF-8
RoxygenNote: 7.1.0
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/dearseq
git_branch: RELEASE_3_11
git_last_commit: 958f6e1
git_last_commit_date: 2020-04-27
Date/Publication: 2020-04-27
NeedsCompilation: no
Packaged: 2020-04-28 07:26:12 UTC; biocbuild
Author: Denis Agniel [aut],
  Boris P. Hejblum [aut, cre],
  Marine Gauthier [aut]
Maintainer: Boris P. Hejblum <boris.hejblum@u-bordeaux.fr>
Built: R 4.0.0; ; 2020-04-28 18:17:18 UTC; windows
