Package: derfinder
Type: Package
Title: Annotation-agnostic differential expression analysis of RNA-seq
        data at base-pair resolution via the DER Finder approach
Version: 1.14.0
Date: 2018-02-23
Authors@R: c(person("Leonardo", "Collado-Torres", role = c("aut", "cre"), email
    = "lcollado@jhu.edu"), person(c("Alyssa", "C."), "Frazee", role = c("ctb"),
    email = "alyssa.frazee@gmail.com"), person(c("Andrew", "E."), "Jaffe",
    role = "aut", email = "andrew.jaffe@libd.org"), person(c("Jeffrey", "T."),
    "Leek", role = c("aut", "ths"), email = "jtleek@gmail.com"))
Depends: R(>= 3.2)
Imports: BiocGenerics (>= 0.25.1), AnnotationDbi (>= 1.27.9),
        BiocParallel, bumphunter (>= 1.9.2), derfinderHelper (>=
        1.1.0), GenomeInfoDb (>= 1.3.3), GenomicAlignments,
        GenomicFeatures, GenomicFiles, GenomicRanges (>= 1.17.40),
        Hmisc, IRanges (>= 2.3.23), methods, qvalue (>= 1.99.0),
        Rsamtools (>= 1.25.0), rtracklayer, S4Vectors (>= 0.9.38)
Suggests: BiocStyle (>= 2.5.19), biovizBase, devtools (>= 1.6),
        derfinderData (>= 0.99.0), derfinderPlot, DESeq2, ggplot2,
        knitcitations (>= 1.0.1), knitr (>= 1.6), limma, RefManageR,
        rmarkdown (>= 0.3.3), testthat,
        TxDb.Hsapiens.UCSC.hg19.knownGene
VignetteBuilder: knitr
Description: This package provides functions for annotation-agnostic
    differential expression analysis of RNA-seq data. Two implementations of
    the DER Finder approach are included in this package: (1) single base-level
    F-statistics and (2) DER identification at the expressed regions-level.
    The DER Finder approach can also be used to identify differentially bounded
    ChIP-seq peaks.
License: Artistic-2.0
LazyData: true
URL: https://github.com/lcolladotor/derfinder
BugReports: https://support.bioconductor.org/t/derfinder/
biocViews: DifferentialExpression, Sequencing, RNASeq, ChIPSeq,
        DifferentialPeakCalling, Software
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2018-05-01 00:16:05 UTC; biocbuild
Author: Leonardo Collado-Torres [aut, cre],
  Alyssa C. Frazee [ctb],
  Andrew E. Jaffe [aut],
  Jeffrey T. Leek [aut, ths]
Maintainer: Leonardo Collado-Torres <lcollado@jhu.edu>
Built: R 3.4.1; ; 2018-10-23 11:10:19 UTC; unix
