Package: derfinder
Type: Package
Title: Annotation-agnostic differential expression analysis of RNA-seq
        data at base-pair resolution via the DER Finder approach
Version: 1.45.0
Date: 2025-07-21
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), Seqinfo (>= 0.99.2), GenomeInfoDb
        (>= 1.45.9), GenomicAlignments, GenomicFeatures, GenomicFiles,
        GenomicRanges (>= 1.61.1), Hmisc, IRanges (>= 2.3.23), methods,
        qvalue (>= 1.99.0), Rsamtools (>= 2.25.1), 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: 7.3.2
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
Config/pak/sysreqs: make libbz2-dev libicu-dev liblzma-dev libpng-dev
        libxml2-dev libssl-dev xz-utils zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2025-10-29 14:21:48 UTC
RemoteUrl: https://github.com/bioc/derfinder
RemoteRef: HEAD
RemoteSha: 946e0b836856d911d009c8c085da47c521a20a62
NeedsCompilation: no
Packaged: 2026-01-09 21:15:30 UTC; root
Author: Leonardo Collado-Torres [aut, cre] (ORCID:
    <https://orcid.org/0000-0003-2140-308X>),
  Alyssa C. Frazee [ctb],
  Andrew E. Jaffe [aut] (ORCID: <https://orcid.org/0000-0001-6886-1454>),
  Jeffrey T. Leek [aut, ths] (ORCID:
    <https://orcid.org/0000-0002-2873-2671>)
Maintainer: Leonardo Collado-Torres <lcolladotor@gmail.com>
Built: R 4.6.0; ; 2026-01-09 21:22:47 UTC; windows
