Package: derfinder
Type: Package
Title: Annotation-agnostic differential expression analysis of RNA-seq
        data at base-pair resolution via the DER Finder approach
Version: 1.40.0
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)
git_url: https://git.bioconductor.org/packages/derfinder
git_branch: RELEASE_3_20
git_last_commit: 245c1b5
git_last_commit_date: 2024-10-29
Repository: Bioconductor 3.20
Date/Publication: 2024-10-29
NeedsCompilation: no
Packaged: 2024-10-30 00:27:20 UTC; biocbuild
Author: Leonardo Collado-Torres [aut, cre]
    (<https://orcid.org/0000-0003-2140-308X>),
  Alyssa C. Frazee [ctb],
  Andrew E. Jaffe [aut] (<https://orcid.org/0000-0001-6886-1454>),
  Jeffrey T. Leek [aut, ths] (<https://orcid.org/0000-0002-2873-2671>)
Maintainer: Leonardo Collado-Torres <lcolladotor@gmail.com>
Built: R 4.4.2; ; 2025-01-01 09:28:08 UTC; unix
