DESCRIPTION

Package: derfinder
Type: Package
Title: Annotation-agnostic differential expression analysis of RNA-seq data at
    base-pair resolution via the DER Finder approach
Version: 1.39.0
Date: 2021-09-14
Authors@R: c(person("Leonardo", "Collado-Torres", role = c("aut", "cre"), email
    = "lcolladotor@gmail.com", comment = c(ORCID = "0000-0003-2140-308X")),
    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",
    comment = c(ORCID = "0000-0001-6886-1454")), person(c("Jeffrey", "T."),
    "Leek", role = c("aut", "ths"), email = "jtleek@gmail.com",
    comment = c(ORCID = "0000-0002-2873-2671")))
Depends:
    R (>= 3.5.0)
Imports:
    BiocGenerics (>= 0.25.1),
    AnnotationDbi (>= 1.27.9),
    BiocParallel (>= 1.15.15),
    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 (>= 0.23.19),
    stats,
    utils
Suggests:
    BiocStyle (>= 2.5.19),
    sessioninfo,
    derfinderData (>= 0.99.0),
    derfinderPlot,
    DESeq2,
    ggplot2,
    knitr (>= 1.6),
    limma,
    RefManageR,
    rmarkdown (>= 0.3.3),
    testthat (>= 2.1.0),
    TxDb.Hsapiens.UCSC.hg19.knownGene,
    covr
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, ImmunoOncology, Coverage
RoxygenNote: 7.2.3
Encoding: UTF-8
Roxygen: list(markdown = TRUE)